There is no difference between a USB pen drive and a USB flash drive; the names are used interchangeably. They're the same product: a tiny data storage device for computer users to insert into an open Universal Serial Bus port.
The technology press tends to call these portable devices by both of these names, among many other names. Retailers may also call them by either name, and they know customers do as well. Sometimes a pen drive is manufactured in the shape of an actual pen, but that's done more for humor or novelty's sake; it has nothing to do with function.