diff --git a/eslint.config.js b/eslint.config.js
index 461171c5d01..cd4a5f1482b 100644
--- a/eslint.config.js
+++ b/eslint.config.js
@@ -92,7 +92,7 @@ module.exports = [
             "tmp/**",
             "tools/internal-rules/node_modules/**",
             "**/test.js",
-            "!**/.eslintrc.js"
+            "!.eslintrc.js"
         ]
     },
     {
diff --git a/lib/cli.js b/lib/cli.js
index 731a32620e2..afd1e65cbd1 100644
--- a/lib/cli.js
+++ b/lib/cli.js
@@ -143,12 +143,6 @@ async function translateOptions({
             overrideConfig[0].plugins = plugins;
         }
 
-        if (ignorePattern) {
-            overrideConfig.push({
-                ignores: ignorePattern
-            });
-        }
-
     } else {
         overrideConfigFile = config;
 
@@ -187,7 +181,9 @@ async function translateOptions({
         reportUnusedDisableDirectives: reportUnusedDisableDirectives ? "error" : void 0
     };
 
-    if (configType !== "flat") {
+    if (configType === "flat") {
+        options.ignorePatterns = ignorePattern;
+    } else {
         options.resolvePluginsRelativeTo = resolvePluginsRelativeTo;
         options.rulePaths = rulesdir;
         options.useEslintrc = eslintrc;
diff --git a/lib/eslint/flat-eslint.js b/lib/eslint/flat-eslint.js
index 3a79cef20a1..d5911853172 100644
--- a/lib/eslint/flat-eslint.js
+++ b/lib/eslint/flat-eslint.js
@@ -362,17 +362,6 @@ async function calculateConfigArray(eslint, {
             const negated = pattern.startsWith("!");
             const basePattern = negated ? pattern.slice(1) : pattern;
 
-            /*
-             * Ignore patterns are considered relative to a directory
-             * when the pattern contains a slash in a position other
-             * than the last character. If that's the case, we need to
-             * add the relative ignore path to the current pattern to
-             * get the correct behavior. Otherwise, no change is needed.
-             */
-            if (!basePattern.includes("/") || basePattern.endsWith("/")) {
-                return pattern;
-            }
-
             return (negated ? "!" : "") +
                 path.posix.join(relativeIgnorePath, basePattern);
         });
diff --git a/tests/fixtures/cli/ignore-pattern-relative/.eslintrc.js b/tests/fixtures/cli/ignore-pattern-relative/.eslintrc.js
new file mode 100644
index 00000000000..cfa7c2db15b
--- /dev/null
+++ b/tests/fixtures/cli/ignore-pattern-relative/.eslintrc.js
@@ -0,0 +1,3 @@
+module.exports = {
+    root: true
+};
diff --git a/tests/fixtures/cli/ignore-pattern-relative/eslint.config.js b/tests/fixtures/cli/ignore-pattern-relative/eslint.config.js
new file mode 100644
index 00000000000..e0a30c5dfa3
--- /dev/null
+++ b/tests/fixtures/cli/ignore-pattern-relative/eslint.config.js
@@ -0,0 +1 @@
+module.exports = [];
diff --git a/tests/fixtures/cli/ignore-pattern-relative/subdir/subsubdir/a.js b/tests/fixtures/cli/ignore-pattern-relative/subdir/subsubdir/a.js
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tests/lib/cli.js b/tests/lib/cli.js
index 75a42d0128b..735141758a9 100644
--- a/tests/lib/cli.js
+++ b/tests/lib/cli.js
@@ -798,6 +798,32 @@ describe("cli", () => {
                         assert.strictEqual(exit, 0);
                     });
 
+                    it(`should interpret pattern that contains a slash as relative to cwd with configType:${configType}`, async () => {
+                        process.cwd = () => getFixturePath("cli/ignore-pattern-relative/subdir");
+
+                        /*
+                         * The config file is in `cli/ignore-pattern-relative`, so this would fail
+                         * if `subdir/**` ignore pattern is interpreted as relative to the config base path.
+                         */
+                        const exit = await cli.execute("**/*.js --ignore-pattern subdir/**", null, useFlatConfig);
+
+                        assert.strictEqual(exit, 0);
+
+                        await stdAssert.rejects(
+                            async () => await cli.execute("**/*.js --ignore-pattern subsubdir/*.js", null, useFlatConfig),
+                            /All files matched by '\*\*\/\*\.js' are ignored/u
+                        );
+                    });
+
+                    it(`should interpret pattern that doesn't contain a slash as relative to cwd with configType:${configType}`, async () => {
+                        process.cwd = () => getFixturePath("cli/ignore-pattern-relative/subdir/subsubdir");
+
+                        await stdAssert.rejects(
+                            async () => await cli.execute("**/*.js --ignore-pattern *.js", null, useFlatConfig),
+                            /All files matched by '\*\*\/\*\.js' are ignored/u
+                        );
+                    });
+
                     if (useFlatConfig) {
                         it("should ignore files if the pattern is a path to a directory (with trailing slash)", async () => {
                             const filePath = getFixturePath("cli/syntax-error.js");