Yes, although the details of these are overall shady at best, and the main interest of the Union seems to have involved obstacle and torpedo (mine) clearance rather than attack at least after the initial phases of the war. The one we know of with absolute certainty is the USS Alligator (1861/62), which had two abortive sorties in the record, and at least one redesign and refit [edit: involving paddle vs. screw propulsion, to give you an idea of how much was uncertain at the time; its early plan was one of many to counter the rumored ironclad refit of the ex-frigate Merrimack as Virginia]; search parties have been looking for its wreck off Cape Hatteras in recent years, in another strange parallel to the case of USS Monitor. I haven't heard any announcement that it's been found, but if anyone has, please do update me! Mark K. Ragan, Union and Confederate Submarine Warfare in the Civil War (Madison City, IA: Savas, 1999) seems to be the only effort at encyclopedic recounting that is widely available, and he notes the problems with trying to track down this service in general as being ones of secrecy and irregularity, with later episodes in the war involving unconfirmed sightings of Union submarines in Confederate harbors and requests from flag officers for the provision of submarines to clear mines that have no resolution yes or no in the record. If they were not used for combat purposes, such submarines logically would leave less of an exclamation point than their CSN counterparts.