The robbery took place near Van Ness Avenue and O'Farrell Street at about 4:05 p.m., according to police.
Police said in a news release that plainclothes Muni task force officers "observed the suspect plotting with two other people to rob the victim," a 16-year-old boy who was standing at the bus stop with his sister.
The officers then saw the suspect run up to the victim, demand his property, shove him to the ground and take his cell phone, police said.
Police then chased the suspect into a nearby parking garage and arrested him. The cell phone was recovered.
The boy was booked into juvenile hall for robbery and resisting arrest, police said.
Police said the department is continuing undercover operations on and near Muni lines.