The suspect, 23-year-old Jahlil McNeal, was arrested during a traffic stop on Saturday.
The incident, which happened at the facility in Atlantic City on July 15, was caught on video.
Dog recovering after being dropped over fence at Atlantic County Humane Society
The video shows a man walking up to the Humane Society and tossing a pit bull mix over the fence around 2 a.m.
The dog has very distinct scarring on her back. Shelter staff believe it's an old injury - possibly a burn.
McNeal is accused of doing something similar back in April. In that incident, three pit bull mixes were tossed over the fence.
McNeal is charged with cruelty to animals and several other offenses.