diff --git a/src/prerender/prerender.ts b/src/prerender/prerender.ts
index f04d578a58..221dcec20d 100644
--- a/src/prerender/prerender.ts
+++ b/src/prerender/prerender.ts
@@ -97,6 +97,8 @@ export async function prerender(nitro: Nitro) {
 
   // Start prerendering
   const generatedRoutes = new Set();
+  // Crawled links, keyed by route (relative to `baseURL`), with their original path
+  const crawledLinkPaths = new Map<string, string>();
   const failedRoutes = new Set<PrerenderRoute>();
   const skippedRoutes = new Set();
   const displayedLengthWarns = new Set();
@@ -181,8 +183,12 @@ export async function prerender(nitro: Nitro) {
   const generateRoute = async (route: string) => {
     const start = Date.now();
 
+    // Crawled links are fetched, resolved and written by their original path
+    const crawledPath = crawledLinkPaths.get(route);
+
     // Ensure route is decoded to start with
     route = decodeURI(route);
+    const routePath = crawledPath ? decodeURI(crawledPath) : route;
 
     // Check if we should render route
     if (!canPrerender(route)) {
@@ -195,7 +201,7 @@ export async function prerender(nitro: Nitro) {
     const _route: PrerenderRoute = { route };
 
     // Fetch the route
-    const encodedRoute = encodeURI(route);
+    const encodedRoute = encodeURI(routePath);
 
     const req = toRequest(withBase(encodedRoute, nitro.options.baseURL), {
       headers: [["x-nitro-prerender", encodedRoute]],
@@ -246,14 +252,14 @@ export async function prerender(nitro: Nitro) {
     // Guess route type and populate fileName
     const contentType = res.headers.get("content-type") || "";
     const isImplicitHTML =
-      !route.endsWith(".html") &&
+      !routePath.endsWith(".html") &&
       contentType.includes("html") &&
       !JsonSigRx.test(dataBuff!.subarray(0, 32).toString("utf8"));
-    const routeWithIndex = route.endsWith("/") ? route + "index" : route;
+    const routeWithIndex = routePath.endsWith("/") ? routePath + "index" : routePath;
     const htmlPath =
-      route.endsWith("/") || nitro.options.prerender.autoSubfolderIndex
-        ? joinURL(route, "index.html")
-        : route + ".html";
+      routePath.endsWith("/") || nitro.options.prerender.autoSubfolderIndex
+        ? joinURL(routePath, "index.html")
+        : routePath + ".html";
     _route.fileName = withoutBase(
       isImplicitHTML ? htmlPath : routeWithIndex,
       nitro.options.baseURL
@@ -292,16 +298,19 @@ export async function prerender(nitro: Nitro) {
     }
 
     // Crawl route links
-    if (!_route.error && (isImplicitHTML || route.endsWith(".html"))) {
+    if (!_route.error && (isImplicitHTML || routePath.endsWith(".html"))) {
       const extractedLinks = await extractLinks(
         dataBuff!.toString("utf8"),
-        route,
+        routePath,
         res,
         nitro.options.prerender.crawlLinks ?? false
       );
       for (const _link of extractedLinks) {
-        if (canPrerender(_link)) {
-          routes.add(_link);
+        // Crawled links include `baseURL`, while routes (and `ignore` patterns) are relative to it
+        const link = withoutBase(_link, nitro.options.baseURL);
+        if (canPrerender(link) && !routes.has(link)) {
+          crawledLinkPaths.set(link, _link);
+          routes.add(link);
         }
       }
     }
diff --git a/test/vite/prerender-baseurl-fixture/nitro.config.ts b/test/vite/prerender-baseurl-fixture/nitro.config.ts
new file mode 100644
index 0000000000..64ea97ea70
--- /dev/null
+++ b/test/vite/prerender-baseurl-fixture/nitro.config.ts
@@ -0,0 +1,7 @@
+import { defineConfig } from "nitro";
+
+export default defineConfig({
+  preset: "static",
+  baseURL: "/base/",
+  prerender: { routes: ["/"], crawlLinks: true, ignore: ["/admin"] },
+});
diff --git a/test/vite/prerender-baseurl-fixture/server.ts b/test/vite/prerender-baseurl-fixture/server.ts
new file mode 100644
index 0000000000..a6e6911f45
--- /dev/null
+++ b/test/vite/prerender-baseurl-fixture/server.ts
@@ -0,0 +1,12 @@
+export default {
+  fetch(req: Request) {
+    const { pathname } = new URL(req.url);
+    // Links rendered by an app with `baseURL` include the base
+    const links = ["/base/", "/base/about", "/base/admin", "/base/base/about"]
+      .map((href) => `<a href="${href}">${href}</a>`)
+      .join("");
+    return new Response(`<h1>${pathname}</h1>${links}`, {
+      headers: { "content-type": "text/html" },
+    });
+  },
+};
diff --git a/test/vite/prerender-baseurl-fixture/vite.config.ts b/test/vite/prerender-baseurl-fixture/vite.config.ts
new file mode 100644
index 0000000000..dc884054e6
--- /dev/null
+++ b/test/vite/prerender-baseurl-fixture/vite.config.ts
@@ -0,0 +1,6 @@
+import { defineConfig } from "vite";
+import { nitro } from "nitro/vite";
+
+export default defineConfig({
+  plugins: [nitro()],
+});
diff --git a/test/vite/prerender-baseurl.test.ts b/test/vite/prerender-baseurl.test.ts
new file mode 100644
index 0000000000..3527bb67b6
--- /dev/null
+++ b/test/vite/prerender-baseurl.test.ts
@@ -0,0 +1,49 @@
+import { fileURLToPath } from "node:url";
+import { join } from "node:path";
+import { readFile, rm, mkdir } from "node:fs/promises";
+import { beforeAll, describe, expect, it } from "vitest";
+import { createNitro, build, prepare } from "nitro/builder";
+
+const fixtureDir = fileURLToPath(new URL("./prerender-baseurl-fixture", import.meta.url));
+const outDir = join(fixtureDir, ".tmp");
+
+// https://github.com/nitrojs/nitro/issues/4441
+describe("prerender with baseURL", () => {
+  const routes: string[] = [];
+
+  beforeAll(async () => {
+    await rm(outDir, { recursive: true, force: true });
+    await mkdir(outDir, { recursive: true });
+    const nitro = await createNitro({
+      rootDir: fixtureDir,
+      output: { dir: outDir },
+      builder: "vite",
+    });
+    nitro.hooks.hook("prerender:route", (route) => {
+      routes.push(route.route);
+    });
+    try {
+      await prepare(nitro);
+      await build(nitro);
+    } finally {
+      await nitro.close();
+    }
+  }, 30_000);
+
+  it("renders crawled links once, without the baseURL prefix", () => {
+    expect(routes.sort()).toEqual(["/", "/about", "/base/about"]);
+  });
+
+  it("fetches and writes crawled links by their original path", async () => {
+    const read = (file: string) => readFile(join(outDir, "public", file), "utf8");
+    expect(await read("index.html")).toContain("<h1>/base</h1>");
+    expect(await read("about/index.html")).toContain("<h1>/base/about</h1>");
+    // `/base/base/about` is the `/base/about` route, not a duplicate of `/about`
+    expect(await read("base/about/index.html")).toContain("<h1>/base/base/about</h1>");
+  });
+
+  it("applies `prerender.ignore` to crawled links", () => {
+    expect(routes).not.toContain("/admin");
+    expect(routes).not.toContain("/base/admin");
+  });
+});