I\'ve been using PDFTK Server on OSX pre 10.11 for over a year without any issues running commands on the command line.
After installing OS
work for me install the new one, https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk_server-2.02-mac_osx-10.11-setup.pkg
remove the old pdftk version; search the pdftk from the finder, move to trash and also have pdftk_uninstall.sh done.
$ pdftk -version
pdftk 2.02 a Handy Tool for Manipulating PDF Documents Copyright (c) 2003-13 Steward and Lee, LLC - Please Visit: www.pdftk.com This is free software; see the source code for copying conditions. There is NO warranty, not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.