As of about 5:30 p.m., trains were behind schedule by up to 20 minutes.
The crossing gate problem is forcing trains to travel slowly through the Burlingame area, Caltrain spokeswoman Christine Dunn said.
In addition, the heat wave has prompted Caltrain to enact a "heat restriction" that calls for trains to slow down from their top speed of 79 mph.
Dunn explained that when it is this hot outside, the rails can become soft and be damaged by trains' weight. Slowing down trains reduces pressure on the rails, she said.
Trains will slow to 60 mph between San Francisco and Redwood City, and to 50 mph between Redwood City and San Jose.
Crews are working to resolve the crossing gate problem, Dunn said.
BART is also experiencing systemwide delays because of the heat.