Earlier, a report surfaced that the 51-year-old Hollywood hunk took the 33-year-old actress out for dinner at The Renaissance at The Manor Hotel last week.
Now, Cruise's representative has denied the rumours, claiming that the report is false, reported E! online.
Cruise ended his five-year marriage to third wife Katie Holmes 15 months ago and since then he has been busy with his work commitments.
Prepon, who shot to fame playing Donna Pinciotti in Fox's hit sitcom That '70s Show, was previously linked to actor Chris Masterson.