Authorities later determined the man was not wearing a bulletproof vest, as was initially reported, and he was not armed and did not threaten anyone.
The man was identified as Don Hamilton, 21, of Simi Valley and he was arrested for being under the influence of a controlled substance.
Investigators say Hamilton was wearing a camouflage vest of a style commonly used by paintball enthusiasts.
The Pacific Surfliner Train 1761 bound for Goleta was delayed around 9 a.m. after passengers and crew reported a man wearing what they thought was a tactical vest was acting strangely and had locked himself in a bathroom onboard.
The train evacuated 93 passengers and five crew members as SWAT responded. Officers were able to make contact with the man and take him into custody.
There were no reports of injuries.
Bomb squad personnel checked and cleared the train before passengers were allowed to continue on their trip.
The train resumed its trip 2 hours and 42 minutes behind schedule. Several other trains in the same area were also delayed, including Amtrak lines 774, 763 and 782.