In conjunction with the Metropolitan Transportation Authority and MTA New York City Transit, the project will use MasterCard's PayPass technology.
The trial will allow customers to pay for their fare at the point of entry by simply tapping their new Citi MasterCard card or payment tag on a specially-designed reader on a subway turnstile.
The payment tag is small enough to fit on to a key chain and removes the need to fumble for cash and coins.
"By taking part in this trial with MasterCard and Citi, the Metropolitan Transportation Authority is continuing its ongoing exploration of electronic payment technology," said Metropolitan Transportation Authority executive director Katherine N. Lapp.
"Contactless payments hold the promise of simplifying fare payment for customers who travel throughout the MTA network, while also providing for operating efficiencies and cost savings," she added.
The aim of the trial is to assess the speed and convenience offered by contactless payment to New York's busy commuters, according to TJ Sharkey of MasterCard International.
"As anyone who has ever commuted through the subway system knows well, time is a critical factor," he added.
The trial will take place at select Lexington Avenue Line 4 5 6 stations.