diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 307fae5396e..57b9e10b253 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 - Rename command "CodeQL: Trim Overlay Base Cache" to "CodeQL: Trim Cache to Overlay-Base" for consistency with "CodeQL: Warm Overlay-Base Cache for [...]" commands. [#4204](https://github.com/github/vscode-codeql/pull/4204)
 - Deprecate the setting (`codeQL.runningQueries.saveCache`) that aggressively saved intermediate results to the disk cache. [#4210](https://github.com/github/vscode-codeql/pull/4210)
+- The CodeQL CLI's `bqrs diff` command is now used in the "Compare Results" view. This makes the view faster, more accurate, and fixes a bug where it would error when comparing a large amount of results. [#4194](https://github.com/github/vscode-codeql/pull/4194) & [#4211](https://github.com/github/vscode-codeql/pull/4211)
 
 ## 1.17.6 - 24 October 2025
 
diff --git a/extensions/ql-vscode/src/codeql-cli/cli-version.ts b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
index ebd30cbdb62..15a6616cb1a 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli-version.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
@@ -11,6 +11,7 @@ interface VersionResult {
 
 export interface CliFeatures {
   queryServerRunQueries?: boolean;
+  bqrsDiffResultSets?: boolean;
 }
 
 export interface VersionAndFeatures {
diff --git a/extensions/ql-vscode/src/codeql-cli/cli.ts b/extensions/ql-vscode/src/codeql-cli/cli.ts
index 493391d5eb3..e17e1ac198c 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli.ts
@@ -41,6 +41,12 @@ import { ExitCodeError, getCliError } from "./cli-errors";
 import { UserCancellationException } from "../common/vscode/progress";
 import type { LanguageClient } from "vscode-languageclient/node";
 
+/**
+ * The oldest version of the CLI that we support. This is used to determine
+ * whether to show a warning about the CLI being too old on startup.
+ */
+export const OLDEST_SUPPORTED_CLI_VERSION = new SemVer("2.20.7");
+
 /**
  * The version of the SARIF format that we are using.
  */
@@ -205,6 +211,7 @@ interface BqrsDecodeOptions {
 
 interface BqrsDiffOptions {
   retainResultSets?: string[];
+  resultSets?: Array<[string, string]>;
 }
 
 type OnLineCallback = (line: string) => Promise<string | undefined>;
@@ -273,8 +280,6 @@ export class CodeQLCliServer implements Disposable {
   /** Path to current codeQL executable, or undefined if not running yet. */
   codeQlPath: string | undefined;
 
-  cliConstraints = new CliVersionConstraint(this);
-
   /**
    * When set to true, ignore some modal popups and assume user has clicked "yes".
    */
@@ -1279,6 +1284,12 @@ export class CodeQLCliServer implements Disposable {
         ...(options?.retainResultSets
           ? ["--retain-result-sets", options.retainResultSets.join(",")]
           : []),
+        ...(options?.resultSets
+          ? options.resultSets.flatMap(([left, right]) => [
+              "--result-sets",
+              `${left},${right}`,
+            ])
+          : []),
         bqrsPath1,
         bqrsPath2,
       ],
@@ -1816,6 +1827,11 @@ export class CodeQLCliServer implements Disposable {
   public async setUseExtensionPacks(useExtensionPacks: boolean) {
     await this.cliConfig.setUseExtensionPacks(useExtensionPacks);
   }
+
+  /** Checks if the CLI supports a specific feature. */
+  public async supportsFeature(feature: keyof CliFeatures): Promise<boolean> {
+    return (await this.getFeatures())[feature] === true;
+  }
 }
 
 /**
@@ -1922,17 +1938,3 @@ export function shouldDebugQueryServer() {
 function shouldDebugCliServer() {
   return isEnvTrue("CLI_SERVER_JAVA_DEBUG");
 }
-
-export class CliVersionConstraint {
-  // The oldest version of the CLI that we support. This is used to determine
-  // whether to show a warning about the CLI being too old on startup.
-  public static OLDEST_SUPPORTED_CLI_VERSION = new SemVer("2.20.7");
-
-  constructor(private readonly cli: CodeQLCliServer) {
-    /**/
-  }
-
-  async supportsQueryServerRunQueries(): Promise<boolean> {
-    return (await this.cli.getFeatures()).queryServerRunQueries === true;
-  }
-}
diff --git a/extensions/ql-vscode/src/compare/compare-view.ts b/extensions/ql-vscode/src/compare/compare-view.ts
index 32e943f4e26..4ab42794d33 100644
--- a/extensions/ql-vscode/src/compare/compare-view.ts
+++ b/extensions/ql-vscode/src/compare/compare-view.ts
@@ -19,6 +19,7 @@ import type { CodeQLCliServer } from "../codeql-cli/cli";
 import type { DatabaseManager } from "../databases/local-databases";
 import { jumpToLocation } from "../databases/local-databases/locations";
 import type { BqrsInfo, BqrsResultSetSchema } from "../common/bqrs-cli-types";
+// eslint-disable-next-line import/no-deprecated
 import resultsDiff from "./resultsDiff";
 import type { CompletedLocalQueryInfo } from "../query-results";
 import { assertNever, getErrorMessage } from "../common/helpers-pure";
@@ -403,13 +404,18 @@ export class CompareView extends AbstractWebview<
       toResultSetName,
     );
 
-    // If the result set names are the same, we use `bqrs diff`. This is more
-    // efficient, but we can't use it in general as it does not support
-    // comparing different result sets.
-    if (fromResultSetName === toResultSetName) {
+    // We use `bqrs diff` when the `--result-sets` option is supported, or when
+    // the result set names are the same (in which case we don't need the
+    // option).
+    const supportsBqrsDiffResultSets =
+      await this.cliServer.supportsFeature("bqrsDiffResultSets");
+    if (supportsBqrsDiffResultSets || fromResultSetName === toResultSetName) {
       const { uniquePath1, uniquePath2, cleanup } =
         await this.cliServer.bqrsDiff(fromPath, toPath, {
           retainResultSets: [],
+          resultSets: supportsBqrsDiffResultSets
+            ? [[fromResultSetName, toResultSetName]]
+            : [],
         });
       try {
         const uniqueInfo1 = await this.cliServer.bqrsInfo(uniquePath1);
@@ -443,10 +449,13 @@ export class CompareView extends AbstractWebview<
         await cleanup();
       }
     } else {
+      // Legacy code path: Perform the diff directly in the extension when we
+      // can't use `bqrs diff`.
       const [fromResultSet, toResultSet] = await Promise.all([
         this.getResultSet(fromInfo.schemas, fromResultSetName, fromPath),
         this.getResultSet(toInfo.schemas, toResultSetName, toPath),
       ]);
+      // eslint-disable-next-line import/no-deprecated
       return resultsDiff(fromResultSet, toResultSet);
     }
   }
diff --git a/extensions/ql-vscode/src/compare/resultsDiff.ts b/extensions/ql-vscode/src/compare/resultsDiff.ts
index a0b240a05ac..cf5d2505c51 100644
--- a/extensions/ql-vscode/src/compare/resultsDiff.ts
+++ b/extensions/ql-vscode/src/compare/resultsDiff.ts
@@ -18,6 +18,10 @@ import type { RawResultSet } from "../common/raw-result-types";
  *  1. number of columns do not match
  *  2. If either query is empty
  *  3. If the queries are 100% disjoint
+ *
+ * @deprecated This function is only used when the `bqrs diff` command does not
+ * support `--result-sets`. It should be removed when all supported CLI versions
+ * support this option.
  */
 export default function resultsDiff(
   fromResults: RawResultSet,
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index c53516185f5..b92cb25a4dd 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -21,7 +21,10 @@ import {
   activate as archiveFilesystemProvider_activate,
   zipArchiveScheme,
 } from "./common/vscode/archive-filesystem-provider";
-import { CliVersionConstraint, CodeQLCliServer } from "./codeql-cli/cli";
+import {
+  CodeQLCliServer,
+  OLDEST_SUPPORTED_CLI_VERSION,
+} from "./codeql-cli/cli";
 import {
   ADD_DATABASE_SOURCE_TO_WORKSPACE_SETTING,
   addDatabaseSourceToWorkspace,
@@ -451,29 +454,19 @@ export async function activate(
 
     let unsupportedWarningShown = false;
     codeQlExtension.cliServer.addVersionChangedListener((ver) => {
-      if (!ver) {
-        return;
-      }
-
-      if (unsupportedWarningShown) {
-        return;
-      }
-
       if (
-        CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION.compare(
-          ver.version,
-        ) <= 0
+        ver &&
+        !unsupportedWarningShown &&
+        OLDEST_SUPPORTED_CLI_VERSION.compare(ver.version) === 1
       ) {
-        return;
+        void showAndLogWarningMessage(
+          extLogger,
+          `You are using an unsupported version of the CodeQL CLI (${ver.version.toString()}). ` +
+            `The minimum supported version is ${OLDEST_SUPPORTED_CLI_VERSION.toString()}. ` +
+            `Please upgrade to a newer version of the CodeQL CLI.`,
+        );
+        unsupportedWarningShown = true;
       }
-
-      void showAndLogWarningMessage(
-        extLogger,
-        `You are using an unsupported version of the CodeQL CLI (${ver.version.toString()}). ` +
-          `The minimum supported version is ${CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION.toString()}. ` +
-          `Please upgrade to a newer version of the CodeQL CLI.`,
-      );
-      unsupportedWarningShown = true;
     });
 
     // Expose the CodeQL CLI features to the extension context under `codeQL.cliFeatures.*`.
diff --git a/extensions/ql-vscode/src/query-server/query-server-client.ts b/extensions/ql-vscode/src/query-server/query-server-client.ts
index c17f4212d73..b7134d2f481 100644
--- a/extensions/ql-vscode/src/query-server/query-server-client.ts
+++ b/extensions/ql-vscode/src/query-server/query-server-client.ts
@@ -101,7 +101,7 @@ export class QueryServerClient extends DisposableObject {
    * queries at once.
    */
   async supportsRunQueriesMethod(): Promise<boolean> {
-    return await this.cliServer.cliConstraints.supportsQueryServerRunQueries();
+    return await this.cliServer.supportsFeature("queryServerRunQueries");
   }
 
   /** Stops the query server by disposing of the current server process. */