We have a GIT Repository on our TFS 2017 OnPremise Installation (Version 15.117.26714.0) with CodeSearch installed.
As per default, CodeSearch is only indexing and searching in the default Branch of the GIT Repository (as it is stated in this How To: Use Code Search Article).
Code Search can index multiple branches in a Git repository - by default it indexes files in only the default branch of your Git repositories (usually this is the master branch). Specify up to five additional branches for each repository that you want Code Search to index in the Options section of the Version Control tab in the Settings page.
I want to setup multiple branches for the CodeSearch to search in, but I can't find such an option at the place where the article says. There are only the two checkboxes you can see in the attached picture.
I am Admin on the TFS - could this still be an issue of permissions?
This has just been enabled in VSTS so it has not made it to on-prem TFS yet. See the October 6 release notes. It is not yet specified when it will make it into TFS, but with 2018 development over is will probably be TFS 2018 Update 1 at the earliest.