Getting the same thing...

Obviously, we need a bit more information, e.g. what OS version you are running on.

I'm running El Capitan. Was forced to downgrade and now it works

the issue here is rootless and the default gem home conflicting

How to slove it ? I get the same thing:-(

Also on OS X El Capitan and getting the same error. Any known resolution without downgrading?

Installing CocoaPods on OS X 10.11 and macOS 10.12

These instructions were tested on all betas and the final release of El Capitan, also on betas of Sierra.

Custom GEM_HOME

This is the solution when you are receiving the "Operation not permitted" error.

$ mkdir -p $HOME/Software/ruby
$ export GEM_HOME=$HOME/Software/ruby
$ gem install cocoapods
[...]
1 gem installed
$ export PATH=$PATH:$HOME/Software/ruby/bin
$ pod --version
0.37.2

Standard system installation

For whatever reason, the rootless stuff seems less restrictive when one simply upgrades the system. I could sudo gem install cocoapods just fine on a machine upgraded from 10.10 - however, binstubs are no longer installed into /usr/bin:

$ sudo gem install cocoapods
[...]
1 gem installed
$ export PATH=$PATH:/Library/Ruby/bin
$ pod --version
0.37.2

We have heard from some users that they receive this error when doing a system-wide installation:

ERROR: While executing gem ... (Errno::EPERM)
Operation not permitted - /usr/bin/pod

This happens when you have updated the rubygems gem of your system ruby installation, but this can be solved by passing -n /usr/local/bin to the install command, so that the pod executable gets installed there. The issue here is that the default gem that ships with the system has a customised binary directory, but any newer version you install (e.g. via gem update --system) does not.

Note: I've locked the issue to collaborators so that these instructions don't get buried for now.