diff --git a/packages/app/src/cli/commands/app/execute.ts b/packages/app/src/cli/commands/app/execute.ts
index 9dfa85c342..64e21185f9 100644
--- a/packages/app/src/cli/commands/app/execute.ts
+++ b/packages/app/src/cli/commands/app/execute.ts
@@ -28,6 +28,7 @@ export default class Execute extends AppLinkedCommand {
       variables: flags.variables,
       outputFile: flags['output-file'],
       ...(flags.version && {version: flags.version}),
+      ...(flags.header && {headers: flags.header}),
     })
 
     return {app: appContextResult.app}
diff --git a/packages/app/src/cli/flags.ts b/packages/app/src/cli/flags.ts
index e9561dada8..048744046a 100644
--- a/packages/app/src/cli/flags.ts
+++ b/packages/app/src/cli/flags.ts
@@ -106,4 +106,9 @@ export const operationFlags = {
     description: 'The file name where results should be written, instead of STDOUT.',
     env: 'SHOPIFY_FLAG_OUTPUT_FILE',
   }),
+  header: Flags.string({
+    description: 'Custom HTTP header to include with the request, in "Key: Value" format. Can be specified multiple times.',
+    env: 'SHOPIFY_FLAG_HEADER',
+    multiple: true,
+  }),
 }
diff --git a/packages/app/src/cli/services/execute-operation.test.ts b/packages/app/src/cli/services/execute-operation.test.ts
index 8f420b7331..73f5c40e8a 100644
--- a/packages/app/src/cli/services/execute-operation.test.ts
+++ b/packages/app/src/cli/services/execute-operation.test.ts
@@ -62,7 +62,11 @@ describe('executeOperation', () => {
       session: mockAdminSession,
       variables: undefined,
       version: '2024-07',
-      responseOptions: {handleErrors: false},
+      responseOptions: {
+        handleErrors: false,
+        onResponse: expect.any(Function),
+      },
+      addedHeaders: undefined,
     })
   })
 
@@ -251,4 +255,205 @@ describe('executeOperation', () => {
       }),
     )
   })
+
+  test('passes custom headers correctly when provided', async () => {
+    const query = 'query { shop { name } }'
+    const headers = ['X-Custom-Header: custom-value', 'Authorization: Bearer token123']
+    const mockResult = {data: {shop: {name: 'Test Shop'}}}
+    vi.mocked(adminRequestDoc).mockResolvedValue(mockResult)
+
+    await executeOperation({
+      organization: mockOrganization,
+      remoteApp: mockRemoteApp,
+      storeFqdn,
+      query,
+      headers,
+    })
+
+    expect(adminRequestDoc).toHaveBeenCalledWith(
+      expect.objectContaining({
+        addedHeaders: {
+          'X-Custom-Header': 'custom-value',
+          Authorization: 'Bearer token123',
+        },
+      }),
+    )
+  })
+
+  test('throws AbortError when header format is invalid (missing colon)', async () => {
+    const query = 'query { shop { name } }'
+    const headers = ['InvalidHeader']
+
+    await expect(
+      executeOperation({
+        organization: mockOrganization,
+        remoteApp: mockRemoteApp,
+        storeFqdn,
+        query,
+        headers,
+      }),
+    ).rejects.toThrow(/Invalid header format/)
+  })
+
+  test('throws AbortError when header key is empty', async () => {
+    const query = 'query { shop { name } }'
+    const headers = [': value-only']
+
+    await expect(
+      executeOperation({
+        organization: mockOrganization,
+        remoteApp: mockRemoteApp,
+        storeFqdn,
+        query,
+        headers,
+      }),
+    ).rejects.toThrow(/Invalid header format/)
+  })
+
+  test('handles headers with whitespace correctly', async () => {
+    const query = 'query { shop { name } }'
+    const headers = ['  X-Header  :  value with spaces  ']
+    const mockResult = {data: {shop: {name: 'Test Shop'}}}
+    vi.mocked(adminRequestDoc).mockResolvedValue(mockResult)
+
+    await executeOperation({
+      organization: mockOrganization,
+      remoteApp: mockRemoteApp,
+      storeFqdn,
+      query,
+      headers,
+    })
+
+    expect(adminRequestDoc).toHaveBeenCalledWith(
+      expect.objectContaining({
+        addedHeaders: {
+          'X-Header': 'value with spaces',
+        },
+      }),
+    )
+  })
+
+  test('allows empty header value', async () => {
+    const query = 'query { shop { name } }'
+    const headers = ['X-Empty-Header:']
+    const mockResult = {data: {shop: {name: 'Test Shop'}}}
+    vi.mocked(adminRequestDoc).mockResolvedValue(mockResult)
+
+    await executeOperation({
+      organization: mockOrganization,
+      remoteApp: mockRemoteApp,
+      storeFqdn,
+      query,
+      headers,
+    })
+
+    expect(adminRequestDoc).toHaveBeenCalledWith(
+      expect.objectContaining({
+        addedHeaders: {
+          'X-Empty-Header': '',
+        },
+      }),
+    )
+  })
+
+  test('includes response extensions in output when present', async () => {
+    const query = 'query { shop { name } }'
+    const mockResult = {shop: {name: 'Test Shop'}}
+    const mockExtensions = {cost: {requestedQueryCost: 1, actualQueryCost: 1}}
+
+    vi.mocked(adminRequestDoc).mockImplementation(async (options) => {
+      // Simulate the onResponse callback being called with extensions
+      if (options.responseOptions?.onResponse) {
+        options.responseOptions.onResponse({
+          data: mockResult,
+          extensions: mockExtensions,
+          headers: new Headers(),
+          status: 200,
+        } as any)
+      }
+      return mockResult
+    })
+
+    const mockOutput = mockAndCaptureOutput()
+
+    await executeOperation({
+      organization: mockOrganization,
+      remoteApp: mockRemoteApp,
+      storeFqdn,
+      query,
+    })
+
+    const output = mockOutput.info()
+    const parsedOutput = JSON.parse(output)
+
+    expect(parsedOutput).toEqual({
+      data: mockResult,
+      extensions: mockExtensions,
+    })
+  })
+
+  test('outputs only data when no extensions are present', async () => {
+    const query = 'query { shop { name } }'
+    const mockResult = {shop: {name: 'Test Shop'}}
+
+    vi.mocked(adminRequestDoc).mockImplementation(async (options) => {
+      // Simulate the onResponse callback being called without extensions
+      if (options.responseOptions?.onResponse) {
+        options.responseOptions.onResponse({
+          data: mockResult,
+          extensions: undefined,
+          headers: new Headers(),
+          status: 200,
+        } as any)
+      }
+      return mockResult
+    })
+
+    const mockOutput = mockAndCaptureOutput()
+
+    await executeOperation({
+      organization: mockOrganization,
+      remoteApp: mockRemoteApp,
+      storeFqdn,
+      query,
+    })
+
+    const output = mockOutput.info()
+    const parsedOutput = JSON.parse(output)
+
+    // Should output just the result, not wrapped in {data: ...}
+    expect(parsedOutput).toEqual(mockResult)
+  })
+
+  test('includes extensions in file output when present', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const outputFile = joinPath(tmpDir, 'results.json')
+      const query = 'query { shop { name } }'
+      const mockResult = {shop: {name: 'Test Shop'}}
+      const mockExtensions = {cost: {requestedQueryCost: 1, actualQueryCost: 1}}
+
+      vi.mocked(adminRequestDoc).mockImplementation(async (options) => {
+        if (options.responseOptions?.onResponse) {
+          options.responseOptions.onResponse({
+            data: mockResult,
+            extensions: mockExtensions,
+            headers: new Headers(),
+            status: 200,
+          } as any)
+        }
+        return mockResult
+      })
+
+      await executeOperation({
+        organization: mockOrganization,
+        remoteApp: mockRemoteApp,
+        storeFqdn,
+        query,
+        outputFile,
+      })
+
+      const expectedContent = JSON.stringify({data: mockResult, extensions: mockExtensions}, null, 2)
+      expect(writeFile).toHaveBeenCalledWith(outputFile, expectedContent)
+    })
+  })
 })
diff --git a/packages/app/src/cli/services/execute-operation.ts b/packages/app/src/cli/services/execute-operation.ts
index aa3d46149b..69fa8b5ba2 100644
--- a/packages/app/src/cli/services/execute-operation.ts
+++ b/packages/app/src/cli/services/execute-operation.ts
@@ -21,6 +21,7 @@ interface ExecuteOperationInput {
   variables?: string
   outputFile?: string
   version?: string
+  headers?: string[]
 }
 
 async function parseVariables(variables?: string): Promise<{[key: string]: unknown} | undefined> {
@@ -37,8 +38,47 @@ async function parseVariables(variables?: string): Promise<{[key: string]: unkno
   }
 }
 
+function parseHeaders(headers?: string[]): {[header: string]: string} | undefined {
+  if (!headers || headers.length === 0) return undefined
+
+  const parsedHeaders: {[header: string]: string} = {}
+
+  for (const header of headers) {
+    const separatorIndex = header.indexOf(':')
+    if (separatorIndex === -1) {
+      throw new AbortError(
+        outputContent`Invalid header format: ${outputToken.yellow(header)}`,
+        'Headers must be in "Key: Value" format.',
+      )
+    }
+
+    const key = header.slice(0, separatorIndex).trim()
+    const value = header.slice(separatorIndex + 1).trim()
+
+    if (!key) {
+      throw new AbortError(
+        outputContent`Invalid header format: ${outputToken.yellow(header)}`,
+        "Header key can't be empty.",
+      )
+    }
+
+    parsedHeaders[key] = value
+  }
+
+  return parsedHeaders
+}
+
 export async function executeOperation(input: ExecuteOperationInput): Promise<void> {
-  const {organization, remoteApp, storeFqdn, query, variables, version: userSpecifiedVersion, outputFile} = input
+  const {
+    organization,
+    remoteApp,
+    storeFqdn,
+    query,
+    variables,
+    version: userSpecifiedVersion,
+    outputFile,
+    headers,
+  } = input
 
   const adminSession = await createAdminSessionAsApp(remoteApp, storeFqdn)
 
@@ -56,10 +96,13 @@ export async function executeOperation(input: ExecuteOperationInput): Promise<vo
   })
 
   const parsedVariables = await parseVariables(variables)
+  const parsedHeaders = parseHeaders(headers)
 
   validateSingleOperation(query)
 
   try {
+    let extensions: unknown
+
     const result = await renderSingleTask({
       title: outputContent`Executing GraphQL operation`,
       task: async () => {
@@ -68,13 +111,20 @@ export async function executeOperation(input: ExecuteOperationInput): Promise<vo
           session: adminSession,
           variables: parsedVariables,
           version,
-          responseOptions: {handleErrors: false},
+          responseOptions: {
+            handleErrors: false,
+            onResponse: (response) => {
+              extensions = response.extensions
+            },
+          },
+          addedHeaders: parsedHeaders,
         })
       },
       renderOptions: {stdout: process.stderr},
     })
 
-    const resultString = JSON.stringify(result, null, 2)
+    const output = extensions ? {data: result, extensions} : result
+    const resultString = JSON.stringify(output, null, 2)
 
     if (outputFile) {
       await writeFile(outputFile, resultString)
diff --git a/packages/cli-kit/src/public/node/api/admin.ts b/packages/cli-kit/src/public/node/api/admin.ts
index 107d91686f..6cf8d8a175 100644
--- a/packages/cli-kit/src/public/node/api/admin.ts
+++ b/packages/cli-kit/src/public/node/api/admin.ts
@@ -62,6 +62,8 @@ export interface AdminRequestOptions<TResult, TVariables extends Variables> {
   responseOptions?: GraphQLResponseOptions<TResult>
   /** Custom request behaviour for retries and timeouts. */
   preferredBehaviour?: RequestModeInput
+  /** Custom HTTP headers to include with the request. */
+  addedHeaders?: {[header: string]: string}
 }
 
 /**
@@ -73,14 +75,14 @@ export interface AdminRequestOptions<TResult, TVariables extends Variables> {
 export async function adminRequestDoc<TResult, TVariables extends Variables>(
   options: AdminRequestOptions<TResult, TVariables>,
 ): Promise<TResult> {
-  const {query, session, variables, version, responseOptions, preferredBehaviour} = options
+  const {query, session, variables, version, responseOptions, preferredBehaviour, addedHeaders: customHeaders} = options
 
   let apiVersion = version ?? LatestApiVersionByFQDN.get(session.storeFqdn)
   if (!apiVersion) {
     apiVersion = await fetchLatestSupportedApiVersion(session, preferredBehaviour)
   }
   let storeDomain = session.storeFqdn
-  const addedHeaders = themeAccessHeaders(session)
+  const addedHeaders = {...themeAccessHeaders(session), ...customHeaders}
 
   if (serviceEnvironment() === 'local') {
     addedHeaders['x-forwarded-host'] = storeDomain