diff --git a/doc_src/cmds/fish.rst b/doc_src/cmds/fish.rst
index 01929d863..d82d3e912 100644
--- a/doc_src/cmds/fish.rst
+++ b/doc_src/cmds/fish.rst
@@ -31,7 +31,9 @@ The following options are available:
 
 - ``-n`` or ``--no-execute`` do not execute any commands, only perform syntax checking
 
-- ``-p`` or ``--profile=PROFILE_FILE`` when fish exits, output timing information on all executed commands to the specified file
+- ``-p`` or ``--profile=PROFILE_FILE`` when fish exits, output timing information on all executed commands to the specified file. This excludes time spent starting up and reading the configuration.
+
+- ``--profile-startup=PROFILE_FILE`` will write timing information for fish's startup to the specified file. This is useful to profile your configuration.
 
 - ``-P`` or ``--private`` enables :ref:`private mode <private-mode>`, so fish will not access old or store new history.
 
diff --git a/share/completions/fish.fish b/share/completions/fish.fish
index 63c55536f..149a18a94 100644
--- a/share/completions/fish.fish
+++ b/share/completions/fish.fish
@@ -5,7 +5,8 @@ complete -c fish -s v -l version -d "Display version and exit"
 complete -c fish -s n -l no-execute -d "Only parse input, do not execute"
 complete -c fish -s i -l interactive -d "Run in interactive mode"
 complete -c fish -s l -l login -d "Run as a login shell"
-complete -c fish -s p -l profile -d "Output profiling information to specified file" -r
+complete -c fish -s p -l profile -d "Output profiling information (excluding startup) to a file" -r
+complete -c fish -s p -l profile-startup -d "Output startup profiling information to a file" -r
 complete -c fish -s d -l debug -d "Specify debug categories" -x -a "(fish --print-debug-categories | string replace ' ' \t)"
 complete -c fish -s o -l debug-output -d "Where to direct debug output to" -rF
 complete -c fish -s D -l debug-stack-frames -d "Show specified # of frames with debug output" -x -a "(seq 128)\t\n"
diff --git a/src/fish.cpp b/src/fish.cpp
index f5e198d14..b601cba8c 100644
--- a/src/fish.cpp
+++ b/src/fish.cpp
@@ -67,6 +67,7 @@ class fish_cmd_opts_t {
     std::string debug_output;
     // File path for profiling output, or empty for none.
     std::string profile_output;
+    std::string profile_startup_output;
     // Commands to be executed in place of interactive shell.
     std::vector<std::string> batch_cmds;
     // Commands to execute after the shell's config has been read.
@@ -274,6 +275,7 @@ static int fish_parse_opt(int argc, char **argv, fish_cmd_opts_t *opts) {
         {"print-rusage-self", no_argument, nullptr, 1},
         {"print-debug-categories", no_argument, nullptr, 2},
         {"profile", required_argument, nullptr, 'p'},
+        {"profile-startup", required_argument, nullptr, 3},
         {"private", no_argument, nullptr, 'P'},
         {"help", no_argument, nullptr, 'h'},
         {"version", no_argument, nullptr, 'v'},
@@ -353,7 +355,14 @@ static int fish_parse_opt(int argc, char **argv, fish_cmd_opts_t *opts) {
                 exit(0);
             }
             case 'p': {
+                // "--profile" - this does not activate profiling right away,
+                // rather it's done after startup is finished.
                 opts->profile_output = optarg;
+                break;
+            }
+            case 3: {
+                // With "--profile-startup" we immediately turn profiling on.
+                opts->profile_startup_output = optarg;
                 g_profiling_active = true;
                 break;
             }
@@ -479,6 +488,18 @@ int main(int argc, char **argv) {
     // Stomp the exit status of any initialization commands (issue #635).
     parser.set_last_statuses(statuses_t::just(STATUS_CMD_OK));
 
+    // If we're profiling startup to a separate file, write it now.
+    if (!opts.profile_startup_output.empty()
+        && opts.profile_startup_output != opts.profile_output) {
+        parser.emit_profiling(opts.profile_startup_output.c_str());
+
+        // If we are profiling both, ensure the startup data only
+        // ends up in the startup file.
+        parser.clear_profiling();
+    }
+
+    g_profiling_active = !opts.profile_output.empty();
+
     // Run post-config commands specified as arguments, if any.
     if (!opts.postconfig_cmds.empty()) {
         res = run_command_list(parser, &opts.postconfig_cmds, {});
@@ -544,7 +565,7 @@ int main(int argc, char **argv) {
     restore_term_mode();
     restore_term_foreground_process_group_for_exit();
 
-    if (g_profiling_active) {
+    if (!opts.profile_output.empty()) {
         parser.emit_profiling(opts.profile_output.c_str());
     }
 
diff --git a/src/parser.cpp b/src/parser.cpp
index fe4a7bdc1..0c22b0ac9 100644
--- a/src/parser.cpp
+++ b/src/parser.cpp
@@ -272,6 +272,10 @@ static void print_profile(const std::deque<profile_item_t> &items, FILE *out) {
     }
 }
 
+void parser_t::clear_profiling() {
+    profile_items.clear();
+}
+
 void parser_t::emit_profiling(const char *path) const {
     // Save profiling information. OK to not use CLO_EXEC here because this is called while fish is
     // exiting (and hence will not fork).
diff --git a/src/parser.h b/src/parser.h
index aec1e934c..c93aa5ccd 100644
--- a/src/parser.h
+++ b/src/parser.h
@@ -400,6 +400,9 @@ class parser_t : public std::enable_shared_from_this<parser_t> {
     /// If profiling is not active, this returns nullptr.
     profile_item_t *create_profile_item();
 
+    /// Remove the profiling items.
+    void clear_profiling();
+
     /// Output profiling data to the given filename.
     void emit_profiling(const char *path) const;
 
diff --git a/tests/checks/invocation.fish b/tests/checks/invocation.fish
index 005d3e501..a8c7cbb35 100644
--- a/tests/checks/invocation.fish
+++ b/tests/checks/invocation.fish
@@ -56,3 +56,25 @@ $fish -c 'string escape y$argv' -c 'string escape x$argv' 1 2 3
 
 # Should just do nothing.
 $fish --no-execute
+
+set -l tmp (mktemp -d)
+$fish --profile $tmp/normal.prof --profile-startup $tmp/startup.prof -ic exit
+
+# This should be the full file - just the one command we gave explicitly!
+cat $tmp/normal.prof
+# CHECK: Time{{\s+}}Sum{{\s+}}Command
+# CHECK: {{\d+\s+\d+\s+>}} exit
+
+string match -rq "builtin source " < $tmp/startup.prof
+and echo matched
+# CHECK: matched
+
+# See that sending both profiles to the same file works.
+$fish --profile $tmp/full.prof --profile-startup $tmp/full.prof -c 'echo thisshouldneverbeintheconfig'
+# CHECK: thisshouldneverbeintheconfig
+string match -rq "builtin source " < $tmp/full.prof
+and echo matched
+# CHECK: matched
+string match -rq "echo thisshouldneverbeintheconfig" < $tmp/full.prof
+and echo matched
+# CHECK: matched