Caltrain averages about one fatality a month, but they say the circumstances of this incident are unusual, because it involved two people.
The northbound train hit the two pedestrians at about 5:45 p.m., Caltrain spokeswoman Christine Dunn said.
One of the pedestrians was killed while the other was taken to a hospital with injuries that Dunn did not reveal the extent of.
The tracks didn't reopen until shortly before 8 p.m., necessitating a bus bridge between the Sunnyvale, Lawrence and Santa Clara stations and causing delays of up to an hour.
There were 70 people on board the train at the time of the accident, Dunn said. Ridership was light because of the Martin Luther King Jr. holiday.
This is the first Caltrain fatality of 2014. Last year, there were 13 fatalities on Caltrain tracks, Dunn said.
The station reopened a few hours later, but while the scene is now clear, the investigation into what happened, is just beginning.
ABC7 News reporter Lilian Kim contributed to this report.