The name derives from the Lithuanian word pelėdnagis (literally 'one with owl's claws') which means 'ham-fisted, dummy'.[2]
Pelėdnagiai has been known since 1659. There was the Pelėdnagiai manor (some of its buildings are still present nearby the Nevėžis river) and watermill.[3] During the Soviet era Pelėdnagiai largely developed as it was a central settlement of Kėdainiai forestry farm and an administration of the Directorate of Land Development and Building (Lithuanian: Melioracijos statybos valdyba, MSV).[4]