The special carriage, which started operating on Monday, runs from 7.30am to 9.30am on the Saikyo Line. This line does a loop around Tokyo and is notorious for groping due to the relatively long distance between stations.
A women's car during evening rush hour has been in operation since July 2002 on the Saikyo Line, whose stops include Japan's busiest station Shinjuku, the entertainment district of Shibuya and central Tokyo Station.
A police report in February said groping on Tokyo trains had tripled over the past eight years. It urged rail firms to set up more women-only cars.
"We are going to study whether we will expand to other lines in the future," a spokesman for the East Japan Railway Co, which operates the Saikyo Line, said.
Other big cities in Japan such as Osaka have already introduced women-only cars during morning rush hour.
"We are going to study whether we will expand to other lines in the future"
A spokesman for the East Japan Railway Co
But Tokyo presented more logistical problems due to its large number of lines, which carry a million people a day.
A number of other railway companies in Tokyo are due to start women-only cars in May on their busiest lines or on rapid trains which tend to be more crowded than local trains.
Police said 2201 cases of groping and more serious sexual assault took place last year on trains, with one-third of the victims being high-school girls.
The cases led to 1886 arrests, with offenders' ages ranging from 14 to 80.