The blockade was called to demand a separate Kamatapur state and Scheduled Tribe status for the Koch Rajbongshis.
The D N Rajdhani Express and Bangalore Express were stopped at New Bongagigaon station for several hours while the UP Kamrup Express was halted at Chirang during the protest.
Senior civil, police and railway officials urged the AAKRSU activists to lift the blockade.
The blockade was lifted after 2 PM and train services have since resumed, the sources added.