diff --git a/.changeset/funny-phones-grab.md b/.changeset/funny-phones-grab.md
new file mode 100644
index 000000000..e6ae86d64
--- /dev/null
+++ b/.changeset/funny-phones-grab.md
@@ -0,0 +1,21 @@
+---
+'@graphql-hive/gateway-runtime': patch
+---
+
+Introduce `deduplicateHeaders` option for `propagateHeaders` configuration to control header handling behavior when multiple subgraphs return the same header
+
+When `deduplicateHeaders` is enabled (set to `true`), only the last value from subgraphs will be set for each header. When disabled (default `false`), all values are appended.
+
+The `set-cookie` header is always appended regardless of this setting, as per HTTP standards.
+
+```ts
+import { defineConfig } from '@graphql-hive/gateway'
+export const gatewayConfig = defineConfig({
+  propagateHeaders: {
+    deduplicateHeaders: true, // default: false
+    fromSubgraphsToClient({ response }) {
+      // ...
+    }
+  }
+})
+```
diff --git a/packages/runtime/src/plugins/usePropagateHeaders.ts b/packages/runtime/src/plugins/usePropagateHeaders.ts
index c98b8a795..0864ef98f 100644
--- a/packages/runtime/src/plugins/usePropagateHeaders.ts
+++ b/packages/runtime/src/plugins/usePropagateHeaders.ts
@@ -14,6 +14,16 @@ interface FromSubgraphsToClientPayload<TContext extends Record<string, any>> {
 }
 
 export interface PropagateHeadersOpts<TContext extends Record<string, any>> {
+  /**
+   * When multiple subgraphs send the same header, should they be deduplicated?
+   * If so, the last subgraphs's header will be _set_ and propagated; otherwise,
+   * all headers will _appended_ and propagated.
+   *
+   * The only exception is `set-cookie`, which is always appended.
+   *
+   * @default false
+   */
+  deduplicateHeaders?: boolean;
   fromClientToSubgraphs?: (
     payload: FromClientToSubgraphsPayload<TContext>,
   ) =>
@@ -118,7 +128,15 @@ export function usePropagateHeaders<TContext extends Record<string, any>>(
           const value = headers[key];
           if (value) {
             for (const v of value) {
-              response.headers.append(key, v);
+              if (
+                !opts.deduplicateHeaders ||
+                key === 'set-cookie' // only set-cookie allows duplicated headers
+              ) {
+                response.headers.append(key, v);
+              } else {
+                // deduplicate headers active
+                response.headers.set(key, v);
+              }
             }
           }
         }
diff --git a/packages/runtime/tests/propagateHeaders.spec.ts b/packages/runtime/tests/propagateHeaders.spec.ts
index 1ec00e32a..d486da7ff 100644
--- a/packages/runtime/tests/propagateHeaders.spec.ts
+++ b/packages/runtime/tests/propagateHeaders.spec.ts
@@ -425,5 +425,281 @@ describe('usePropagateHeaders', () => {
         );
       }
     });
+    it('should deduplicate non-cookie headers from multiple subgraphs when deduplicateHeaders is true', async () => {
+      const upstream1WithDuplicates = createYoga({
+        schema: createSchema({
+          typeDefs: /* GraphQL */ `
+            type Query {
+              hello1: String
+            }
+          `,
+          resolvers: {
+            Query: {
+              hello1: () => 'world1',
+            },
+          },
+        }),
+        plugins: [
+          {
+            onResponse: ({ response }) => {
+              response.headers.set('x-shared-header', 'value-from-upstream1');
+              response.headers.append('set-cookie', 'cookie1=value1');
+            },
+          },
+        ],
+      }).fetch;
+      const upstream2WithDuplicates = createYoga({
+        schema: createSchema({
+          typeDefs: /* GraphQL */ `
+            type Query {
+              hello2: String
+            }
+          `,
+          resolvers: {
+            Query: {
+              hello2: () => 'world2',
+            },
+          },
+        }),
+        plugins: [
+          {
+            onResponse: ({ response }) => {
+              response.headers.set('x-shared-header', 'value-from-upstream2');
+              response.headers.append('set-cookie', 'cookie2=value2');
+            },
+          },
+        ],
+      }).fetch;
+      await using gateway = createGatewayRuntime({
+        supergraph: () => {
+          return getUnifiedGraphGracefully([
+            {
+              name: 'upstream1',
+              schema: createSchema({
+                typeDefs: /* GraphQL */ `
+                  type Query {
+                    hello1: String
+                  }
+                `,
+              }),
+              url: 'http://localhost:4001/graphql',
+            },
+            {
+              name: 'upstream2',
+              schema: createSchema({
+                typeDefs: /* GraphQL */ `
+                  type Query {
+                    hello2: String
+                  }
+                `,
+              }),
+              url: 'http://localhost:4002/graphql',
+            },
+          ]);
+        },
+        propagateHeaders: {
+          deduplicateHeaders: true,
+          fromSubgraphsToClient({ response }) {
+            const cookies = response.headers.getSetCookie();
+            const sharedHeader = response.headers.get('x-shared-header');
+
+            const returns: Record<string, string | string[]> = {
+              'set-cookie': cookies,
+            };
+
+            if (sharedHeader) {
+              returns['x-shared-header'] = sharedHeader;
+            }
+
+            return returns;
+          },
+        },
+        plugins: () => [
+          useCustomFetch((url, options, context, info) => {
+            switch (url) {
+              case 'http://localhost:4001/graphql':
+                // @ts-expect-error TODO: url can be a string, not only an instance of URL
+                return upstream1WithDuplicates(url, options, context, info);
+              case 'http://localhost:4002/graphql':
+                // @ts-expect-error TODO: url can be a string, not only an instance of URL
+                return upstream2WithDuplicates(url, options, context, info);
+              default:
+                throw new Error('Invalid URL');
+            }
+          }),
+        ],
+        logging: isDebug(),
+      });
+      const response = await gateway.fetch('http://localhost:4000/graphql', {
+        method: 'POST',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify({
+          query: /* GraphQL */ `
+            query {
+              hello1
+              hello2
+            }
+          `,
+        }),
+      });
+
+      const resJson = await response.json();
+      expect(resJson).toEqual({
+        data: {
+          hello1: 'world1',
+          hello2: 'world2',
+        },
+      });
+
+      // Non-cookie headers should be deduplicated (only the last value is kept)
+      expect(response.headers.get('x-shared-header')).toBe(
+        'value-from-upstream2',
+      );
+
+      // set-cookie headers should still be aggregated (not deduplicated)
+      expect(response.headers.get('set-cookie')).toBe(
+        'cookie1=value1, cookie2=value2',
+      );
+    });
+    it('should append all non-cookie headers from multiple subgraphs when deduplicateHeaders is false', async () => {
+      const upstream1WithDuplicates = createYoga({
+        schema: createSchema({
+          typeDefs: /* GraphQL */ `
+            type Query {
+              hello1: String
+            }
+          `,
+          resolvers: {
+            Query: {
+              hello1: () => 'world1',
+            },
+          },
+        }),
+        plugins: [
+          {
+            onResponse: ({ response }) => {
+              response.headers.set('x-shared-header', 'value-from-upstream1');
+              response.headers.append('set-cookie', 'cookie1=value1');
+            },
+          },
+        ],
+      }).fetch;
+      const upstream2WithDuplicates = createYoga({
+        schema: createSchema({
+          typeDefs: /* GraphQL */ `
+            type Query {
+              hello2: String
+            }
+          `,
+          resolvers: {
+            Query: {
+              hello2: () => 'world2',
+            },
+          },
+        }),
+        plugins: [
+          {
+            onResponse: ({ response }) => {
+              response.headers.set('x-shared-header', 'value-from-upstream2');
+              response.headers.append('set-cookie', 'cookie2=value2');
+            },
+          },
+        ],
+      }).fetch;
+      await using gateway = createGatewayRuntime({
+        supergraph: () => {
+          return getUnifiedGraphGracefully([
+            {
+              name: 'upstream1',
+              schema: createSchema({
+                typeDefs: /* GraphQL */ `
+                  type Query {
+                    hello1: String
+                  }
+                `,
+              }),
+              url: 'http://localhost:4001/graphql',
+            },
+            {
+              name: 'upstream2',
+              schema: createSchema({
+                typeDefs: /* GraphQL */ `
+                  type Query {
+                    hello2: String
+                  }
+                `,
+              }),
+              url: 'http://localhost:4002/graphql',
+            },
+          ]);
+        },
+        propagateHeaders: {
+          deduplicateHeaders: false,
+          fromSubgraphsToClient({ response }) {
+            const cookies = response.headers.getSetCookie();
+            const sharedHeader = response.headers.get('x-shared-header');
+
+            const returns: Record<string, string | string[]> = {
+              'set-cookie': cookies,
+            };
+
+            if (sharedHeader) {
+              returns['x-shared-header'] = sharedHeader;
+            }
+
+            return returns;
+          },
+        },
+        plugins: () => [
+          useCustomFetch((url, options, context, info) => {
+            switch (url) {
+              case 'http://localhost:4001/graphql':
+                // @ts-expect-error TODO: url can be a string, not only an instance of URL
+                return upstream1WithDuplicates(url, options, context, info);
+              case 'http://localhost:4002/graphql':
+                // @ts-expect-error TODO: url can be a string, not only an instance of URL
+                return upstream2WithDuplicates(url, options, context, info);
+              default:
+                throw new Error('Invalid URL');
+            }
+          }),
+        ],
+        logging: isDebug(),
+      });
+      const response = await gateway.fetch('http://localhost:4000/graphql', {
+        method: 'POST',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify({
+          query: /* GraphQL */ `
+            query {
+              hello1
+              hello2
+            }
+          `,
+        }),
+      });
+
+      const resJson = await response.json();
+      expect(resJson).toEqual({
+        data: {
+          hello1: 'world1',
+          hello2: 'world2',
+        },
+      });
+
+      // Non-cookie headers should NOT be deduplicated (all values are appended)
+      expect(response.headers.get('x-shared-header')).toBe(
+        'value-from-upstream1, value-from-upstream2',
+      );
+
+      // set-cookie headers should be aggregated as usual
+      expect(response.headers.get('set-cookie')).toBe(
+        'cookie1=value1, cookie2=value2',
+      );
+    });
   });
 });