The first time Jay's apartment is shown is in Entry #19, but it is assumed the computer in his living room is where he views all the tapes in the first season. During Entry#19, Jay tries to sleep, only for Masky to show up and wander his room, before leaving. Jay vanishes as well along with him, and walks back into the room and falls asleep almost immediately, however Jay has no idea where he went or when that happened as he doesn't remember ever being up.
Entry #19.5 is also the location where Jay examines the items he's acquired at Brian's house. He notes the bullet casing missing and the pill bottle empty, probably due to Masky.
In Entry #24 Jay gets up once again and leaves his room, however he had set cameras around his house just to videotape himself. In this instance, something weird happens, as he enters the door to leave his room, but does not come out his living room. Instead he walks into a completely black room, and is gone for 3 hours before returning. It's unknown where he went, although it is more than likely that the Operator caused him to Slenderwalk.
By the events of Entry #25, he's shown to have left his home and is looking for a safe place, when he gets a notice from someone he knows (never stated who) to turn on the news. In the broadcast his apartment has been set on fire. Although Jay never gets an answer, it's believed this was due to the Operator's powers.