Penguin Group says if the program is successful, it could offer e-books to libraries nationwide.
Until now, Penguin had been one of four major publishers that didn't make e-books available to libraries.
The Wall Street Journal reports that under the deal with Penguin and distributor 3M, the New York and Brooklyn systems will get the e-books six months after the titles go on sale in stores and online.
New York-based Penguin stopped selling e-books to libraries last fall because of unspecified security concerns.
The New York Public Library serves Manhattan, Staten Island and the Bronx.
The Queens Library hopes to join the pilot, pending passage of the city budget.