Stephen Colbert is going scorched earth on Robert F. Kennedy Jr. … after the U.S. Health and Human Services Secretary announced he’s slashing $500 million in vaccine research funding this week.

The ‘Late Show’ host didn’t hold back Wednesday night … joking he was about to deliver a “measured, nonpartisan response” — then unloading on RFK Jr. with “F*** you, you ‘roid-addled nepo-carnie.”

Colbert flips the bird to the camera … and the audience roars with applause.

He explains RFK Jr. is axing 22 projects involving mRNA technology — the latest vaccine science research, which helped speed a COVID vaccine during the pandemic … Colbert compared that to navigating a road trip to Six Flags using the stars in the sky instead of GPS.

Colbert plays a clip of Kennedy justifying the cuts, claiming … “Most of these shots are for flu or COVID, but as the pandemic showed us, mRNA vaccines don’t perform well against viruses that infect the upper respiratory tract.”

The CBS host claps back with, “Counterpoint, f*** you, you road-munching, luddite, human Slim Jim. You’re gonna kill people.” Colbert throws up the middle finger to the camera again, and the crowd goes crazy.

Clearly, Colbert isn’t afraid to take shots after announcing his show is getting the axe.