They have been identified as 47-year-old Joseph Rozario and his 8-year-old son Fabian.
Police are now trying to piece together what led up to what is being investigated as a murder-suicide.
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The call for a welfare check came just after 6 p.m. Thursday evening when the wife and mother came home but couldn't get inside.
When police arrived at the residence on the 500 block of Heritage Oak Drive in Lower Makefield Township, they saw a child lying on the floor inside the home.
Officers kicked the door in and found both father and son suffering from gunshot wounds to their heads.
"They checked the house and saw a little boy on the floor. They immediately kicked the door and found the father also. We don't have a motive at this point, obviously probably domestic," said Lower Makefield Township Police Chief Kenneth Coluzzi.
No one else was home at the time of the shooting.
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The mother of the family was notified of the situation, police say.
Fabian was a student at Afton Elementary School in the Pennsbury School District.
Grief counselors will be available at the school from 10 a.m. to 1 p.m. on Saturday.