diff --git a/src/cli.zig b/src/cli.zig
index e2a62330cc..5f6f7026cc 100644
--- a/src/cli.zig
+++ b/src/cli.zig
@@ -690,13 +690,26 @@ pub const Command = struct {
                         const original_argv_len = bun.argv.len;
                         var argv_list = std.array_list.Managed([:0]const u8).fromOwnedSlice(bun.default_allocator, bun.argv);
                         try bun.appendOptionsEnv(graph.compile_exec_argv, &argv_list, bun.default_allocator);
-                        bun.argv = argv_list.items;
+
+                        // Store the full argv including user arguments
+                        const full_argv = argv_list.items;
+                        const num_exec_argv_options = full_argv.len -| original_argv_len;
 
                         // Calculate offset: skip executable name + all exec argv options
-                        offset_for_passthrough = if (bun.argv.len > 1) 1 + (bun.argv.len -| original_argv_len) else 0;
+                        offset_for_passthrough = if (full_argv.len > 1) 1 + num_exec_argv_options else 0;
+
+                        // Temporarily set bun.argv to only include executable name + exec_argv options.
+                        // This prevents user arguments like --version/--help from being intercepted
+                        // by Bun's argument parser (they should be passed through to user code).
+                        bun.argv = full_argv[0..@min(1 + num_exec_argv_options, full_argv.len)];
 
                         // Handle actual options to parse.
-                        break :brk try Command.init(allocator, log, .AutoCommand);
+                        const result = try Command.init(allocator, log, .AutoCommand);
+
+                        // Restore full argv so passthrough calculation works correctly
+                        bun.argv = full_argv;
+
+                        break :brk result;
                     }
 
                     context_data = .{
diff --git a/test/bundler/compile-argv.test.ts b/test/bundler/compile-argv.test.ts
index 6d7ea8d20f..50b32fa5fb 100644
--- a/test/bundler/compile-argv.test.ts
+++ b/test/bundler/compile-argv.test.ts
@@ -175,4 +175,105 @@ describe("bundler", () => {
       stdout: /SUCCESS: user arguments properly passed with exec argv present/,
     },
   });
+
+  // Test that --version and --help flags are passed through to user code (issue #26082)
+  // When compile-exec-argv is used, user flags like --version should NOT be intercepted by Bun
+  itBundled("compile/CompileExecArgvVersionHelpPassthrough", {
+    compile: {
+      execArgv: ["--smol"],
+    },
+    backend: "cli",
+    files: {
+      "/entry.ts": /* js */ `
+        // Test that --version and --help are passed through to user code, not intercepted by Bun
+        const args = process.argv.slice(2);
+        console.log("User args:", JSON.stringify(args));
+
+        if (args.includes("--version")) {
+          console.log("APP_VERSION:1.0.0");
+        } else if (args.includes("-v")) {
+          console.log("APP_VERSION:1.0.0");
+        } else if (args.includes("--help")) {
+          console.log("APP_HELP:This is my app help");
+        } else if (args.includes("-h")) {
+          console.log("APP_HELP:This is my app help");
+        } else {
+          console.log("NO_FLAG_MATCHED");
+        }
+      `,
+    },
+    run: {
+      args: ["--version"],
+      stdout: /APP_VERSION:1\.0\.0/,
+    },
+  });
+
+  // Test with -v short flag
+  itBundled("compile/CompileExecArgvShortVersionPassthrough", {
+    compile: {
+      execArgv: ["--smol"],
+    },
+    backend: "cli",
+    files: {
+      "/entry.ts": /* js */ `
+        const args = process.argv.slice(2);
+        if (args.includes("-v")) {
+          console.log("APP_VERSION:1.0.0");
+        } else {
+          console.log("FAIL: -v not found in args:", args);
+          process.exit(1);
+        }
+      `,
+    },
+    run: {
+      args: ["-v"],
+      stdout: /APP_VERSION:1\.0\.0/,
+    },
+  });
+
+  // Test with --help flag
+  itBundled("compile/CompileExecArgvHelpPassthrough", {
+    compile: {
+      execArgv: ["--smol"],
+    },
+    backend: "cli",
+    files: {
+      "/entry.ts": /* js */ `
+        const args = process.argv.slice(2);
+        if (args.includes("--help")) {
+          console.log("APP_HELP:my custom help");
+        } else {
+          console.log("FAIL: --help not found in args:", args);
+          process.exit(1);
+        }
+      `,
+    },
+    run: {
+      args: ["--help"],
+      stdout: /APP_HELP:my custom help/,
+    },
+  });
+
+  // Test with -h short flag
+  itBundled("compile/CompileExecArgvShortHelpPassthrough", {
+    compile: {
+      execArgv: ["--smol"],
+    },
+    backend: "cli",
+    files: {
+      "/entry.ts": /* js */ `
+        const args = process.argv.slice(2);
+        if (args.includes("-h")) {
+          console.log("APP_HELP:my custom help");
+        } else {
+          console.log("FAIL: -h not found in args:", args);
+          process.exit(1);
+        }
+      `,
+    },
+    run: {
+      args: ["-h"],
+      stdout: /APP_HELP:my custom help/,
+    },
+  });
 });