diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1996672d53..83766b0741 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -237,6 +237,16 @@
 
 ### Bug Fixes
 
+* Make `--only-rule` and `only_rules:` actually run custom rules.
+  `activateCustomRuleIdentifiers` previously only expanded custom rules for
+  the `only_rules:` config key when `custom_rules` itself was listed,
+  never for the `--only-rule` command-line flag or for an individual
+  custom rule identifier. As a result `--only-rule custom_rules`,
+  `--only-rule <a_custom_rule>` and `only_rules: [<a_custom_rule>]`
+  silently produced no violations. Now any of these enables the parent
+  `custom_rules` rule together with the requested custom rules.  
+  [Chupik](https://github.com/Chupik)
+  
 * Recognize `isolated` as an isolation modifier in `modifier_order`, so it can
   be ordered via the `isolation` entry in `preferred_modifier_order`.  
   [leno23](https://github.com/leno23)
diff --git a/Source/SwiftLintFramework/Configuration/Configuration+RulesMode.swift b/Source/SwiftLintFramework/Configuration/Configuration+RulesMode.swift
index cfc5902261..ff71222647 100644
--- a/Source/SwiftLintFramework/Configuration/Configuration+RulesMode.swift
+++ b/Source/SwiftLintFramework/Configuration/Configuration+RulesMode.swift
@@ -116,18 +116,38 @@ public extension Configuration {
         }
 
         internal func activateCustomRuleIdentifiers(allRulesWrapped: [ConfigurationRuleWrapper]) -> Self {
-            // In the only mode, if the custom rules rule is enabled, all custom rules are also enabled implicitly
-            // This method makes the implicitly explicit
+            // In the "only" modes the parent `custom_rules` rule and the individual custom rules are
+            // entangled: enabling `custom_rules` implies enabling every custom rule, and enabling any
+            // individual custom rule requires the parent `custom_rules` rule to be enabled too.
+            // This method makes those implicit relations explicit so that both `only_rules` (config)
+            // and `--only-rule` (command line) behave consistently — previously `--only-rule` left
+            // custom rules silently disabled, and `only_rules: [<individual_custom_rule>]` did too.
             switch self {
-            case let .onlyConfiguration(onlyRules) where onlyRules.contains {
-                $0 == CustomRules.identifier
-            }:
-                let customRulesRule = allRulesWrapped.customRules
-                return .onlyConfiguration(onlyRules.union(Set(customRulesRule?.customRuleIdentifiers ?? [])))
+            case let .onlyConfiguration(onlyRules):
+                return .onlyConfiguration(Self.withCustomRulesActivated(onlyRules, allRulesWrapped: allRulesWrapped))
+
+            case let .onlyCommandLine(onlyRules):
+                return .onlyCommandLine(Self.withCustomRulesActivated(onlyRules, allRulesWrapped: allRulesWrapped))
 
             default:
                 return self
             }
         }
+
+        private static func withCustomRulesActivated(
+            _ onlyRules: Set<String>,
+            allRulesWrapped: [ConfigurationRuleWrapper]
+        ) -> Set<String> {
+            let customRuleIdentifiers = Set(allRulesWrapped.customRules?.customRuleIdentifiers ?? [])
+            var onlyRules = onlyRules
+            if onlyRules.contains(CustomRules.identifier) {
+                // `custom_rules` is enabled → enable all of its custom rules.
+                onlyRules.formUnion(customRuleIdentifiers)
+            } else if !onlyRules.isDisjoint(with: customRuleIdentifiers) {
+                // At least one individual custom rule is enabled → enable the parent `custom_rules` rule.
+                onlyRules.insert(CustomRules.identifier)
+            }
+            return onlyRules
+        }
     }
 }
diff --git a/Tests/FrameworkTests/OnlyRuleCustomRulesTests.swift b/Tests/FrameworkTests/OnlyRuleCustomRulesTests.swift
new file mode 100644
index 0000000000..0bba477161
--- /dev/null
+++ b/Tests/FrameworkTests/OnlyRuleCustomRulesTests.swift
@@ -0,0 +1,74 @@
+@testable import SwiftLintCore
+@testable import SwiftLintFramework
+import TestHelpers
+import XCTest
+
+/// Tests that custom (regex) rules can be selected via `--only-rule` from the command line and via
+/// `only_rules:` from a configuration file.
+///
+/// Before the fix, `activateCustomRuleIdentifiers` only expanded custom rules for the
+/// `.onlyConfiguration` mode (and even there, only when `custom_rules` itself was the listed
+/// identifier), so:
+///
+/// * `--only-rule custom_rules` ran the parent rule but had every individual custom rule filtered
+///   out, producing zero violations.
+/// * `--only-rule my_custom_rule` left the parent `custom_rules` rule out of the resulting rule set
+///   entirely, so the custom rule never executed.
+/// * `only_rules: [my_custom_rule]` had the same problem as the second case.
+final class OnlyRuleCustomRulesTests: SwiftLintTestCase {
+    /// Instance-scoped so that a non-`Sendable` `[String: Any]` literal is not held as shared
+    /// mutable global state. A `static let` here is rejected by the Swift 6 language mode that
+    /// Bazel CI compiles with.
+    private var customRulesDict: [String: Any] {
+        [
+            "custom_rules": [
+                "rule_a": ["name": "RuleA", "regex": "a", "message": "msg"],
+                "rule_b": ["name": "RuleB", "regex": "b", "message": "msg"],
+            ],
+        ]
+    }
+
+    // MARK: - `--only-rule` from the command line
+
+    func testOnlyRuleFromCommandLineForIndividualCustomRule() throws {
+        let config = try Configuration(dict: customRulesDict, onlyRule: ["rule_a"])
+        let activeCustomRules = activeCustomRuleIdentifiers(in: config)
+        XCTAssertEqual(activeCustomRules, ["rule_a"])
+    }
+
+    func testOnlyRuleFromCommandLineForCustomRulesParentEnablesAll() throws {
+        let config = try Configuration(dict: customRulesDict, onlyRule: ["custom_rules"])
+        let activeCustomRules = activeCustomRuleIdentifiers(in: config)
+        XCTAssertEqual(activeCustomRules, ["rule_a", "rule_b"])
+    }
+
+    func testOnlyRuleFromCommandLineForUnrelatedRuleDoesNotEnableCustomRules() throws {
+        let config = try Configuration(dict: customRulesDict, onlyRule: ["line_length"])
+        XCTAssertNil(
+            config.rules.first(where: { $0 is CustomRules }),
+            "`--only-rule` for an unrelated built-in rule must not pull in the custom_rules parent rule"
+        )
+    }
+
+    // MARK: - `only_rules:` in configuration
+
+    func testOnlyRulesInConfigForIndividualCustomRule() throws {
+        var dict = customRulesDict
+        dict["only_rules"] = ["rule_a"]
+        let config = try Configuration(dict: dict)
+        let activeCustomRules = activeCustomRuleIdentifiers(in: config)
+        XCTAssertEqual(activeCustomRules, ["rule_a"])
+    }
+
+    // MARK: - Helpers
+
+    /// Returns the identifiers of the custom rule configurations that remain active in `config`'s
+    /// `resultingRules`, sorted for deterministic comparison. Empty if the parent `custom_rules`
+    /// rule was filtered out entirely.
+    private func activeCustomRuleIdentifiers(in config: Configuration) -> [String] {
+        guard let customRules = config.rules.first(where: { $0 is CustomRules }) as? CustomRules else {
+            return []
+        }
+        return customRules.configuration.customRuleConfigurations.map(\.identifier).sorted()
+    }
+}