The children, a 1-year-old boy and a 2-year-old girl, were not hurt, according to Columbia Borough Police.
Investigators said it was during a domestic dispute that Frank J. Kellam, of 530 Union St., Columbia, retrieved a .22-caliber rifle and shot out the rear window of the sport utility vehicle.
The incident occurred around 2:15 a.m. at Second and Perry streets.
Kellam is charged with aggravated assault, endangering the welfare of children and persons not to possess firearms, all felonies.
He was arraigned by District Judge Robert Herman and committed to Lancaster County Prison in lieu of $100,000 bail.
According to charging documents, the dispute between Kellam and his girlfriend began earlier in the night when the two got into an argument at a Mountville restaurant.
After the incident at the eatery, the woman drove her Dodge Durango to a friend's home in the 100 block of Perry Street in Columbia, according to the criminal complaint.
Kellam followed her in his Honda Accord, police said. The couple's children were riding in the Durango.
Upon arrival at the Perry Street home, the girlfriend went inside while Kellam remained outside with a male resident of the home, police wrote in the complaint.
While outside, Kellam "was irate" and began kicking the Durango which was parked on Second Street, according to investigators.
The male resident was joined by a female resident of the home, and the two tried to calm Kellam, reminding him that his children were in the SUV, the complaint states.
Kellam then walked to his Honda, retrieved a .22-caliber rifle and fired four to five shots into the back window of the Durango, investigators wrote.
Police said the children were in the second-row seat.
They said the window was shattered and that several bullets traveled to the inside of the SUV.
Kellam fled the scene but was later taken into custody in Lancaster city in a coordinated effort involving Columbia Borough police, U.S. Marshals and state police.