The program, commonly referred to as CHIP, covers roughly 9 million children whose families don't have access to affordable health care, but earn too much to qualify for Medicaid.
Kimmel held his boy Billy, who was born with a heart defect, during his opening monologue and updated fans on his treatment.
Kimmel's son, Billy, had surgery soon after he was born in April and the eight-month-old had another operation last week.
"I've had enough of this", Kimmel said indignantly.
Jimmy - who has kids Katie, 26, and Kevin, 24, with former wife Gina, and three-year-old Jane with wife Molly McNearney - also paid tribute to the "very bright and talented" doctors and nurses who cared for Billy in hospital, and told viewers about a health insurance programme.
Then Kimmel dug his heels into the topic of the night, quickly explaining the history of CHIP: "It's not controversial, it's not a partisan thing. overwhelmingly Democrats and Republicans supported it until now".
More news: Interstellar asteroid checked for alien technology"Now CHIP has become a bargaining chip", said Kimmel.
He went on to explain the Children's Health Insurance Program which, as he stated, "covers around 9 million American kids whose parents made too much money to qualify for Medicaid, but don't have access to affordable coverage due to their jobs, meaning it nearly certainly covers children you know". It's always had bipartisan support.
"This happened because Congress, about 72 days ago, failed to approve funding for CHIP", Kimmel continued. "Imagine getting that letter, literally not knowing how you will afford to save your child's life", he said. "If these were potato chips they were taking away from us, we would be marching in Washington with pitchforks and spears right now".
First the good: "Billy is doing great, by the way". He was one more surgery.
"They say he'll probably be on track to win at least a bronze medal at the Olympics in 2036", Kimmel joked.
