diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4e2efe08..5c7878d4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ A preview of the next release can be installed from
 
 [Babashka](https://github.com/babashka/babashka): Native, fast starting Clojure interpreter for scripting
 
+## Unreleased
+
+- [#1658](https://github.com/babashka/babashka/issues/1658): fix command line parsing for scripts that parse `--version` or `version` etc
+
 ## 1.3.187 (2023-01-09)
 
 - Add `clojure.reflect/reflect`
diff --git a/src/babashka/main.clj b/src/babashka/main.clj
index 76707089..b4f48ddb 100644
--- a/src/babashka/main.clj
+++ b/src/babashka/main.clj
@@ -722,9 +722,10 @@ Use bb run --help to show this help output.
   (let [opt (first options)]
     (if (and opt (and (fs/exists? opt)
                       (not (fs/directory? opt))))
-      [(next options) (assoc opts-map
-                             (if (str/ends-with? opt ".jar")
-                               :jar :file) opt)]
+      [nil (assoc opts-map
+                  (if (str/ends-with? opt ".jar")
+                    :jar :file) opt
+                  :command-line-args (next options))]
       [options opts-map])))
 
 (defn parse-opts
@@ -745,8 +746,7 @@ Use bb run --help to show this help output.
                (and (not (or (:file opts-map)
                              (:jar opts-map)))
                     (.isFile (io/file opt)))
-               (let [[args opts] (parse-file-opt options opts-map)]
-                 (assoc opts :command-line-args args))
+               (parse-file-opt options opts-map)
                (contains? tasks opt)
                (assoc opts-map
                       :run opt
@@ -1146,12 +1146,12 @@ Use bb run --help to show this help output.
                (list* "--jar" bin-jar "--" args)
                args)
         [args opts] (parse-global-opts args)
-        ;; TODO: drop jar file from opts
         [args {:keys [jar file config merge-deps debug] :as opts}]
         (if-not (or (:file opts)
                     (:jar opts))
           (parse-file-opt args opts)
           [args opts])
+        ;; _ (prn :args args :opts opts)
         abs-path #(-> % io/file .getAbsolutePath)
         config (cond
                  config (if (fs/exists? config) (abs-path config)
diff --git a/test-resources/script_with_overlapping_opts.clj b/test-resources/script_with_overlapping_opts.clj
new file mode 100644
index 00000000..5b71e3dc
--- /dev/null
+++ b/test-resources/script_with_overlapping_opts.clj
@@ -0,0 +1 @@
+(prn *command-line-args*)
diff --git a/test/babashka/bb_edn_test.clj b/test/babashka/bb_edn_test.clj
index 96852475..424c17b7 100644
--- a/test/babashka/bb_edn_test.clj
+++ b/test/babashka/bb_edn_test.clj
@@ -388,7 +388,7 @@ even more stuff here\"
       (try
         (spit "uberjar" "#!/usr/bin/env bb\n(+ 1 2 3)")
         (vreset! common/bb-edn '{:tasks {uberjar (+ 1 2 3)}})
-        (is (= "uberjar" (:file (main/parse-opts ["uberjar"]))))
+        (is (= {:file "uberjar", :command-line-args '("--version")} (second (main/parse-opts ["uberjar" "--version"]))))
         (finally (fs/delete "uberjar"))))))
 
 (deftest min-bb-version-test
diff --git a/test/babashka/main_test.clj b/test/babashka/main_test.clj
index 49177045..3ee6ab1b 100644
--- a/test/babashka/main_test.clj
+++ b/test/babashka/main_test.clj
@@ -1,6 +1,7 @@
 (ns babashka.main-test
   {:clj-kondo/config '{:linters {:unresolved-symbol {:exclude [working?]}}}}
   (:require
+   [babashka.fs :as fs]
    [babashka.main :as main]
    [babashka.test-utils :as test-utils]
    [clojure.edn :as edn]
@@ -71,7 +72,9 @@
            (-> (let [[_ opts] (main/parse-file-opt ["-e" "(prn :foo)"] {})]
                  (main/parse-opts ["-e" "(prn :foo)"] opts)))))
     (is (= {:file "foo", :command-line-args ["README.md"]}
-           (main/parse-opts ["README.md"] {:file "foo"})))))
+           (main/parse-opts ["README.md"] {:file "foo"})))
+    (is (= ["--version"] (bb nil (fs/file "test-resources" "script_with_overlapping_opts.clj") "--version")))
+    (is (= ["version"] (bb nil (fs/file "test-resources" "script_with_overlapping_opts.clj") "version")))))
 
 (deftest version-test
   (is (= [1 0 0] (main/parse-version "1.0.0-SNAPSHOT")))