Justice Alexander Owens ruled that McGregor should pay the entire costs of the case which ran for 12 days, and have been estimated at around 1.5 million euros (£1.24 million) according to local media.
In November, a jury at Dublin's High Court awarded damages of 248,603 euros (£206,084) to Nikita Hand, 35, who brought the successful case.
The court was told that McGregor allegedly "brutally raped and battered" Hand in a Dublin hotel in December 2018 but the Irish sports star claimed they had consensual sex.
Although the jury found in Hand's favour in connection with her accusation against McGregor, she lost an assault lawsuit against a second man.
McGregor is one of the biggest stars in the history of the Ultimate Fighting Championship (UFC) mixed martial arts circuit, formerly holding the featherweight and lightweight titles.
In a statement on X after the civil case verdict, McGregor said he intended to appeal.