Desean Walker, 19, and Thomas Nicholas Furman, 18, both of redwood City, were arrested by transit police on suspicion of robbery and assault with great bodily injury, according to Caltrain officials.
The pair was arrested in connection with the March 4 attack that left a 47-year-old man in critical condition at a hospital, officials said.
The victim was attacked by a group of assailants who were trying to rob him as he waited for a southbound train at about 7:30 p.m. that day.
Walker was already in custody on unrelated robbery charges when he was arrested for the Caltrain attack, according to officials.
Both he and Furman are scheduled to be arraigned this afternoon in San Mateo County Superior Court.
Three search warrants were also executed in Redwood City and East Palo Alto in connection with the case, and evidence recovered during the searches has provided investigators with information that they say will help locate other suspects in the case.
"We are confident that everyone will be brought to justice," Dave Triolo, Caltrain's chief of protective services, said in a statement.
"This incident is an extremely rare occurrence in the Caltrain system and we want to deliver a clear message: commit a crime and face a swift and effective response from law enforcement," Triolo said.
Anyone with information about the case is encouraged to contact Detective Victor Lopez at (650) 622-8048.