Crews will be closing the southbound track to install new concrete pads at the crossing, as well as replace worn rails, ties and ballast.
Passengers using Caltrain will board for both north and southbound trains on the northbound platform throughout the weekend.
Tracks and the roadways are scheduled to reopen around 5 a.m. Monday, according to Caltrain.
Drivers are asked to detour around the closure by using Bayswater Avenue.
Caltrain crews will also be working on the California Avenue station in Palo Alto this weekend. A new pedestrian underpass is being constructed, but all work will be done at night to accommodate train schedules.