diff --git a/pkgs/applications/editors/neovim/default.nix b/pkgs/applications/editors/neovim/default.nix
index a3580b1afa7a..27e274326470 100644
--- a/pkgs/applications/editors/neovim/default.nix
+++ b/pkgs/applications/editors/neovim/default.nix
@@ -20,6 +20,13 @@ let
       sha256 = "07ncvgp6xfhiwc6hd7qf7zk28n3yj47p26qj1ji29vqkwnk28y3s";
     };
 
+    patches = [
+      # introduce a system-wide rplugin.vim in addition to the user one
+      # necessary so that nix can handle `UpdateRemotePlugins` for the plugins
+      # it installs. See https://github.com/neovim/neovim/issues/9413.
+      ./system_rplugin_manifest.patch
+    ];
+
     enableParallelBuilding = true;
 
     buildInputs = [
diff --git a/pkgs/applications/editors/neovim/system_rplugin_manifest.patch b/pkgs/applications/editors/neovim/system_rplugin_manifest.patch
new file mode 100644
index 000000000000..f634d3ec056a
--- /dev/null
+++ b/pkgs/applications/editors/neovim/system_rplugin_manifest.patch
@@ -0,0 +1,29 @@
+diff --git a/runtime/autoload/remote/host.vim b/runtime/autoload/remote/host.vim
+index 6266b312b..965fabf1e 100644
+--- a/runtime/autoload/remote/host.vim
++++ b/runtime/autoload/remote/host.vim
+@@ -71,7 +71,8 @@ function! remote#host#RegisterPlugin(host, path, specs) abort
+ 
+   for plugin in plugins
+     if plugin.path == a:path
+-      throw 'Plugin "'.a:path.'" is already registered'
++      " plugin already registered
++      return
+     endif
+   endfor
+ 
+diff --git a/runtime/plugin/rplugin.vim b/runtime/plugin/rplugin.vim
+index 122d8d47f..83fbf8b57 100644
+--- a/runtime/plugin/rplugin.vim
++++ b/runtime/plugin/rplugin.vim
+@@ -54,6 +54,10 @@ function! s:GetManifest() abort
+ endfunction
+ 
+ function! s:LoadRemotePlugins() abort
++  if exists('$NVIM_SYSTEM_RPLUGIN_MANIFEST')
++    let g:system_remote_plugins = fnamemodify($NVIM_SYSTEM_RPLUGIN_MANIFEST, ':p')
++    execute 'source' fnameescape(g:system_remote_plugins)
++  endif
+   let g:loaded_remote_plugins = s:GetManifest()
+   if filereadable(g:loaded_remote_plugins)
+     execute 'source' fnameescape(g:loaded_remote_plugins)
diff --git a/pkgs/applications/editors/neovim/wrapper.nix b/pkgs/applications/editors/neovim/wrapper.nix
index d69e68ac61fc..7d76bc1fd1a0 100644
--- a/pkgs/applications/editors/neovim/wrapper.nix
+++ b/pkgs/applications/editors/neovim/wrapper.nix
@@ -72,7 +72,6 @@ let
         --cmd \"${if withRuby then "let g:ruby_host_prog='$out/bin/nvim-ruby'" else "let g:loaded_ruby_provider=1"}\" " \
         --suffix PATH : ${binPath} \
         ${optionalString withRuby '' --set GEM_HOME ${rubyEnv}/${rubyEnv.ruby.gemPath}'' }
-
       ''
       + optionalString (!stdenv.isDarwin) ''
         # copy and patch the original neovim.desktop file
@@ -92,7 +91,29 @@ let
       '' + optionalString viAlias ''
         ln -s $out/bin/nvim $out/bin/vi
       '' + optionalString (configure != {}) ''
-        wrapProgram $out/bin/nvim --add-flags "-u ${vimUtils.vimrcFile configure}"
+        echo "Generating remote plugin manifest"
+        export NVIM_RPLUGIN_MANIFEST=$out/rplugin.vim
+        # Launch neovim with a vimrc file containing only the generated plugin
+        # code. Pass various flags to disable temp file generation
+        # (swap/viminfo) and redirect errors to stderr.
+        # Only display the log on error since it will contain a few normally
+        # irrelevant messages.
+        if ! $out/bin/nvim \
+          -u ${vimUtils.vimrcFile (configure // { customRC = ""; })} \
+          -i NONE -n \
+          -E -V1rplugins.log -s \
+          +UpdateRemotePlugins +quit! > outfile 2>&1; then
+          cat outfile
+          echo -e "\nGenerating rplugin.vim failed!"
+          exit 1
+        fi
+        unset NVIM_RPLUGIN_MANIFEST
+
+        # this relies on a patched neovim, see
+        # https://github.com/neovim/neovim/issues/9413
+        wrapProgram $out/bin/nvim \
+          --set NVIM_SYSTEM_RPLUGIN_MANIFEST $out/rplugin.vim \
+          --add-flags "-u ${vimUtils.vimrcFile configure}"
       '';
 
     preferLocalBuild = true;
diff --git a/pkgs/misc/vim-plugins/vim-utils.nix b/pkgs/misc/vim-plugins/vim-utils.nix
index cf5eeaec3e33..2a758aa98433 100644
--- a/pkgs/misc/vim-plugins/vim-utils.nix
+++ b/pkgs/misc/vim-plugins/vim-utils.nix
@@ -486,4 +486,12 @@ rec {
       });
     vimrcConfig.vam.pluginDictionaries = [ { names = [ "vim-trailing-whitespace" ]; } ];
   };
+
+  # system remote plugin manifest should be generated, deoplete should be usable
+  # without the user having to do `UpdateRemotePlugins`. To test, launch neovim
+  # and do `:call deoplete#enable()`. It will print an error if the remote
+  # plugin is not registered.
+  test_nvim_with_remote_plugin = neovim.override {
+    configure.pathogen.pluginNames = with vimPlugins; [ deoplete-nvim ];
+  };
 }