30-year-old Todd Caswell was arrested in Rhode Island and extradited to Connecticut after several years of being a fugitive from justice, Connecticut State Police said.
One cow was shot in the face and had to be euthanized, while the other was shot in the back and treated for an infection.
Two other people were involved with the incident and quickly turned themselves in 2013, State Police said.
Caswell received multiple charges including discharge of a firearm, cruelty to animals, and criminal mischief. He was held on a $100,000 bond and appeared in court on Friday.