Police said during the first incident the man performed a sexual act in front of a 22-year-old woman on a city-bound Hurstbridge train at about 7.20pm on March 3.
The man then disembarked the train at Flinders Street Station.
Police said during the second incident the man sat next to a 29-year-old woman at about 10.10pm and performed a sexual act before disembarking the train at Southern Cross Railway Station.
The man, who police said is believed to be responsible for both incidents, was wearing a red baseball cap with a Sydney Swans logo, a grey zip-up hooded jumper, black shorts and dark grey runners.
Police have released photos and CCTV of a man they believe may be able to assist with their enquiries.
The man is perceived to be Caucasian in appearance, with a slim build and short fair hair.