diff --git a/pkgs/applications/misc/zathura/core/default.nix b/pkgs/applications/misc/zathura/core/default.nix
index 78d4d69e1263..84dc14451532 100644
--- a/pkgs/applications/misc/zathura/core/default.nix
+++ b/pkgs/applications/misc/zathura/core/default.nix
@@ -1,6 +1,7 @@
-{ stdenv, fetchurl, makeWrapper, pkgconfig
-, gtk, girara, ncurses, gettext, docutils
-, file, sqlite, glib, texlive, libintl
+{ stdenv, fetchurl, fetchpatch, meson, ninja, makeWrapper, pkgconfig
+, appstream-glib, desktop-file-utils, python3
+, gtk, girara, ncurses, gettext, libxml2
+, file, sqlite, glib, texlive, libintl, libseccomp
 , gtk-mac-integration, synctexSupport ? true
 }:
 
@@ -9,52 +10,42 @@ assert synctexSupport -> texlive != null;
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  name    = "zathura-core-${version}";
-  version = "0.3.8";
+  name = "zathura-core-${version}";
+  version = "0.3.9";
 
   src = fetchurl {
-    url    = "http://pwmt.org/projects/zathura/download/zathura-${version}.tar.gz";
-    sha256 = "0dz5pky3vmf3s2cp2rv1c099gb1s49p9xlgm3ghyy4pzyxc8bgs6";
+    url = "https://pwmt.org/projects/zathura/download/zathura-${version}.tar.xz";
+    sha256 = "0z09kz92a2n8qqv3cy8bx5j5k612g2f9mmh4szqlc7yvi39aax1g";
   };
 
-  icon = ./icon.xpm;
+  patches = [
+    (fetchpatch {
+      url = https://git.pwmt.org/pwmt/zathura/commit/4223464db68529f9a2064ed760fb7746b3c0df6b.patch;
+      sha256 = "004j68b7c8alxzyx0d80lr5i43cgh7lbqm5fx3d77ihci7hdmxnw";
+    })
+  ];
 
   nativeBuildInputs = [
-    pkgconfig libintl
+    meson ninja pkgconfig appstream-glib desktop-file-utils python3.pkgs.sphinx
+    gettext makeWrapper libxml2
   ];
 
   buildInputs = [
-    file gtk girara
-    gettext makeWrapper sqlite glib
+    file gtk girara libintl libseccomp
+    sqlite glib
   ] ++ optional synctexSupport texlive.bin.core
     ++ optional stdenv.isDarwin [ gtk-mac-integration ];
 
-  NIX_CFLAGS_COMPILE = "-I${glib.dev}/include/gio-unix-2.0";
-
-  makeFlags = [
-    "PREFIX=$(out)"
-    "RSTTOMAN=${docutils}/bin/rst2man.py"
-    "VERBOSE=1"
-    "TPUT=${ncurses.out}/bin/tput"
-    (optionalString synctexSupport "WITH_SYNCTEX=1")
-  ];
-
   postInstall = ''
     wrapProgram "$out/bin/zathura" \
-      --prefix PATH ":" "${makeBinPath [ file ]}" \
-      --prefix XDG_CONFIG_DIRS ":" "$out/etc"
-
-    install -Dm644 $icon $out/share/pixmaps/pwmt.xpm
-    mkdir -pv $out/etc
-    echo "set window-icon $out/share/pixmaps/pwmt.xpm" > $out/etc/zathurarc
-    echo "Icon=pwmt" >> $out/share/applications/zathura.desktop
+      --prefix PATH ":" "${makeBinPath [ file ]}"
   '';
 
   meta = {
-    homepage    = http://pwmt.org/projects/zathura/;
+    homepage = https://pwmt.org/projects/zathura/;
     description = "A core component for zathura PDF viewer";
-    license     = licenses.zlib;
-    platforms   = platforms.unix;
+    license = licenses.zlib;
+    platforms = platforms.unix;
     maintainers = with maintainers; [ garbas ];
   };
 }
diff --git a/pkgs/applications/misc/zathura/core/icon.xpm b/pkgs/applications/misc/zathura/core/icon.xpm
deleted file mode 100644
index a863c5ddb090..000000000000
--- a/pkgs/applications/misc/zathura/core/icon.xpm
+++ /dev/null
@@ -1,120 +0,0 @@
-/* XPM */
-static char *freeimage[] = {
-/* width height num_colors chars_per_pixel */
-"16 16 96 2",
-/* colors */
-"   c #1e1e1e",
-" . c #222222",
-" X c #212121",
-" o c #535353",
-" O c #a4a4a4",
-" + c #202020",
-" @ c #252525",
-" # c #3c3c3c",
-" $ c #292929",
-" % c #979797",
-" & c #cccccc",
-" * c #303030",
-" = c #1f1f1f",
-" - c #494949",
-" ; c #dddddd",
-" : c #696969",
-" > c #232323",
-" , c #262626",
-" < c #adadad",
-" 1 c #bbbbbb",
-" 2 c #1d1d1d",
-" 3 c #1c1c1c",
-" 4 c #5e5e5e",
-" 5 c #e8e8e8",
-" 6 c #9c9c9c",
-" 7 c #242424",
-" 8 c #b1b1b1",
-" 9 c #b3b3b3",
-" 0 c #090909",
-" q c #161616",
-" w c #131313",
-" e c #4d4d4d",
-" r c #dedede",
-" t c #afafaf",
-" y c #282828",
-" u c #393939",
-" i c #c4c4c4",
-" p c #dcdcdc",
-" a c #9a9a9a",
-" s c #a2a2a2",
-" d c #ababab",
-" f c #313131",
-" g c #a7a7a7",
-" h c #e4e4e4",
-" j c #f2f2f2",
-" k c #eaeaea",
-" l c #e2e2e2",
-" z c #f0f0f0",
-" x c #d5d5d5",
-" c c #737373",
-" v c #323232",
-" b c #808080",
-" n c #7a7a7a",
-" m c #d3d3d3",
-" M c #e5e5e5",
-" N c #8a8a8a",
-" B c #cbcbcb",
-" V c #b5b5b5",
-" C c #b9b9b9",
-" Z c #272727",
-" A c #b4b4b4",
-" S c #bababa",
-" D c #2d2d2d",
-" F c #414141",
-" G c #444444",
-" H c #f4f4f4",
-" J c #838383",
-" K c #cfcfcf",
-" L c #fafafa",
-" P c #efefef",
-" I c #e3e3e3",
-" U c #8d8d8d",
-" Y c #656565",
-" T c #ffffff",
-" R c #fbfbfb",
-" E c #e9e9e9",
-" W c #bdbdbd",
-" Q c #e1e1e1",
-" ! c #dfdfdf",
-" ~ c #646464",
-" ^ c #3a3a3a",
-" / c #a1a1a1",
-" ( c #999999",
-" ) c #c0c0c0",
-" _ c #3b3b3b",
-" ` c #acacac",
-" ' c #050505",
-" ] c #151515",
-" [ c #1b1b1b",
-" { c #1a1a1a",
-" } c #b2b2b2",
-" | c #a5a5a5",
-".  c #c5c5c5",
-".. c #a6a6a6",
-".X c #bfbfbf",
-".o c #747474",
-/* pixels */
-"                                ",
-"   . . . X X X X . o O + X . .  ",
-"   . . X @ # $ . @ % & * = . .  ",
-"   . .   - ; : > , < 1 2 X . .  ",
-"   . . 3 4 5 6 7 7 8 9 0 q q 3  ",
-"   . + w e r t y u i p a s d 4  ",
-"   X f g h j k p l z z x g c v  ",
-"   X f b n m M N c B V 3 , > X  ",
-"   X X   w V C $ Z A S + $ , .  ",
-"   D F G u S H 1 J K L P I U @  ",
-"   Y T T T R E & W Q ! d g ~ 7  ",
-"   ^ / 6 ( ; ) _ 2 ` 8 ' ] [ X  ",
-"   + > 7 { A } 7 @ |.  $ + . .  ",
-"   X X X ].. 8 Z 7 n.X + X . .  ",
-"   . . . { n.o 7 . @ y X X . .  ",
-"                                "
-};
-