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, according to Lieutenant Daniels. (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")
In the 32nd century, a checkpoint was placed at the entrance to the Mercantile in Requiem, Hima. This checkpoint was manned by regulators who were assisted in their duties by drones. In 3188, Cleveland Booker and Michael Burnham attempted passing through this checkpoint. The drone scanned each of their left sleeves for a piece of technology which identified them as couriers. Unlike Booker, who passed the scan, Burnham failed the scan and was initially denied entrance because she had no identification. After Booker convinced one of the bosses that Burnham had a thing of value (her 23rd century tricorder) which might interest an antique collector of vintage technology, she was admitted into the marketplace. (DIS: "That Hope Is You, Part 1")