Perkins finished the third iteration of the event, started Saturday, in just 13 hours, six minutes and 52 seconds -- nearly three hours better than the last best time.
Some 300 runners from around the world took part in the event blending extreme sport and historic pilgrimage, which this year marked 25 years since the Cold War symbol of the Wall was torn down.
The runners took off on Saturday at 6:00 am (0400 GMT), passing through a rotunda near the famous border crossing Checkpoint Charlie.
The Berlin Wall was designed to stop an exodus of people to the West. It cut through city blocks, neighbourhoods, fields and forests and was shadowed by a heavily mined "death strip", overlooked by watch towers and patrolled by soldiers and dogs.
These days, the path of the Wall is a hiking and cycling trail.