diff --git a/scripts/measure-rpc-rtt.mjs b/scripts/measure-rpc-rtt.mjs
index 9a03609b680e..77734fbba2fc 100644
--- a/scripts/measure-rpc-rtt.mjs
+++ b/scripts/measure-rpc-rtt.mjs
@@ -14,6 +14,7 @@ import { resolveWindowsTaskkillPath } from "./lib/windows-taskkill.mjs";
 
 const DEFAULT_METHODS = ["health", "config.get"];
 const DEFAULT_ITERATIONS = 10;
+const SINGLE_VALUE_FLAGS = new Set(["--iterations", "--methods", "--output-dir", "--repo-root"]);
 /** Maximum time to wait for a spawned gateway to become reachable. */
 export const READY_TIMEOUT_MS = 120_000;
 /** Per-probe timeout used while polling gateway readiness endpoints. */
@@ -74,12 +75,19 @@ export function parseArgs(argv) {
     iterations: DEFAULT_ITERATIONS,
     methods: DEFAULT_METHODS,
   };
+  const seenSingleValueFlags = new Set();
   for (let index = 0; index < argv.length; index += 1) {
     const arg = argv[index];
     if (arg === "--help" || arg === "-h") {
       args.help = true;
       continue;
     }
+    if (SINGLE_VALUE_FLAGS.has(arg)) {
+      if (seenSingleValueFlags.has(arg)) {
+        throw new Error(`${arg} was provided more than once.`);
+      }
+      seenSingleValueFlags.add(arg);
+    }
     if (arg === "--output-dir") {
       args.outputDir = readFlagValue(argv, index, arg);
       index += 1;
diff --git a/test/scripts/measure-rpc-rtt.test.ts b/test/scripts/measure-rpc-rtt.test.ts
index badd3093aa2a..71375067314f 100644
--- a/test/scripts/measure-rpc-rtt.test.ts
+++ b/test/scripts/measure-rpc-rtt.test.ts
@@ -182,6 +182,12 @@ describe("scripts/measure-rpc-rtt.mjs", () => {
     expect(() =>
       parseArgs(["--output-dir", "/tmp/rpc-rtt", "--methods", "health, config.get,health"]),
     ).toThrow("--methods contains duplicate gateway method: health");
+    expect(() => parseArgs(["--output-dir", "/tmp/one", "--output-dir", "/tmp/two"])).toThrow(
+      "--output-dir was provided more than once.",
+    );
+    expect(() =>
+      parseArgs(["--output-dir", "/tmp/rpc-rtt", "--methods", "health", "--methods", "config.get"]),
+    ).toThrow("--methods was provided more than once.");
     for (const value of ["--methods", "-h"]) {
       for (const flag of ["--output-dir", "--repo-root", "--iterations", "--methods"]) {
         expect(() => parseArgs([flag, value, "health"])).toThrow(`${flag} requires a value.`);