A checkpoint was a location where a barrier was established by a security force and people traveling through had to be cleared by members of the force.
In 2063, the crew of the USS Enterprise established defense checkpoints on the ship during their struggle against the Borg. After their interplexing beacon was destroyed, the Borg advanced and overran three of the checkpoints. (Star Trek: First Contact)
In 2267, during the search for the Mother Horta on planet Janus VI, Captain James T. Kirk established a checkpoint on level 23, code-named "Tiger". Administrative head Vanderberg was to assemble his team of miners and rendezvous with the USS Enterprise search parties at this place. (TOS: "The Devil in the Dark")