The league on Thursday announced that Lapointe voluntarily had sought help but wouldn't elaborate. Under terms of the program, team officials are forbidden from discussing details of the case.
The source, speaking on condition of anonymity, said Lapointe has been taking medication to treat depression for several weeks.
Several published reports Friday said teammates and coaches knew of Lapointe's depression but tried to keep it quiet.
"Whatever has been going on, he's decided that this is the best thing to do and he's dealing with it," Flyers general manager Bob Clarke said. "There's nothing else that we can say except that Claude is getting the help he needs and we'll be here when he comes back."
The program's doctors, Dr. Dave Lewis on behalf of the NHL and Dr. Brian Shaw on behalf of the NHL Players' Association, are supervising Lapointe's care, the NHL said in its news release.
The Flyers acquired Lapointe, 35, in March from the New York Islanders for a fifth-round draft pick. This season, he has two goals and two assists for four points and 10 penalty minutes in 19 games.
Lapointe, who plays on the Flyers' fourth line, signed a two-year contract in July.