diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e884a7d2..35a86ae93 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@
 - More of the documentation, including the tutorial, is now available as man pages as well.
 - Local values for `fish_complete_path` and `fish_function_path` are now ignored; only their global values are respected.
 - Empty universal variables may now be exported (#5992).
+- `string split` had a bug where empty strings would be dropped if the output was only empty strings; this has been fixed (#5987).
 
 ### Syntax changes and new commands
 - Brace expansion now only takes place if the braces include a "," or a variable expansion, so things like `git reset HEAD@{0}` now work (#5869).
diff --git a/src/io.cpp b/src/io.cpp
index edbf06e9b..54ead1392 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -31,14 +31,15 @@ void io_pipe_t::print() const {
 void io_bufferfill_t::print() const { std::fwprintf(stderr, L"bufferfill {%d}\n", write_fd_.fd()); }
 
 void io_buffer_t::append_from_stream(const output_stream_t &stream) {
-    if (stream.empty()) return;
+    const separated_buffer_t<wcstring> &input = stream.buffer();
+    if (input.elements().empty()) return;
     scoped_lock locker(append_lock_);
     if (buffer_.discarded()) return;
-    if (stream.buffer().discarded()) {
+    if (input.discarded()) {
         buffer_.set_discard();
         return;
     }
-    buffer_.append_wide_buffer(stream.buffer());
+    buffer_.append_wide_buffer(input);
 }
 
 void io_buffer_t::run_background_fillthread(autoclose_fd_t readfd) {
diff --git a/src/io.h b/src/io.h
index 89fcdc810..79ea595de 100644
--- a/src/io.h
+++ b/src/io.h
@@ -403,8 +403,6 @@ class output_stream_t {
 
     void append_formatv(const wchar_t *format, va_list va) { append(vformat_string(format, va)); }
 
-    bool empty() const { return buffer_.size() == 0; }
-
     wcstring contents() const { return buffer_.newline_serialized(); }
 };
 
diff --git a/src/parse_execution.cpp b/src/parse_execution.cpp
index eff62a4e6..75d7cc7d0 100644
--- a/src/parse_execution.cpp
+++ b/src/parse_execution.cpp
@@ -337,8 +337,9 @@ parse_execution_result_t parse_execution_context_t::run_function_statement(
     int err = builtin_function(*parser, streams, arguments, pstree, body);
     parser->set_last_statuses(statuses_t::just(err));
 
-    if (!streams.err.empty()) {
-        this->report_error(header, L"%ls", streams.err.contents().c_str());
+    wcstring errtext = streams.err.contents();
+    if (!errtext.empty()) {
+        this->report_error(header, L"%ls", errtext.c_str());
         result = parse_execution_errored;
     }
 
diff --git a/tests/checks/string.fish b/tests/checks/string.fish
index c27b6b6c1..6e2ee8ba9 100644
--- a/tests/checks/string.fish
+++ b/tests/checks/string.fish
@@ -498,6 +498,12 @@ end
 count (dualsplit)
 # CHECK: 4
 
+# Ensure we handle empty outputs correctly (#5987)
+count (string split / /)
+# CHECK: 2
+count (echo -ne '\x00\x00\x00' | string split0)
+# CHECK: 3
+
 # string collect
 count (echo one\ntwo\nthree\nfour | string collect)
 count (echo one | string collect)