After 40 years on the federal bench, Judge William G. Young recently experienced what he viewed as a career first, and it didn’t sit well with him.

“I have never seen government racial discrimination like this,” Judge Young said on Monday, excoriating the Trump administration in a lengthy speech from the U.S. District Court in Boston.

In keeping with his usual process, he had ordered a quick trial to debate the merits of two lawsuits challenging some of the government’s cuts to research grants and programs administered by the National Institutes of Health — the first trial in the more than 400 cases contesting nearly all aspects of President Trump’s agenda winding their way through the courts.

The grants at issue, which funded research into diversity-related topics like health disparities in Black and L.G.B.T.Q. communities, were canceled by Mr. Trump and N.I.H. leadership as part of the administration’s efforts to eliminate diversity, equity and inclusion initiatives and roll back transgender rights. Judge Young cast his decision to block the cuts as his duty in following the Constitution.

“I am hesitant to draw this conclusion, but I have an unflinching obligation to draw it: that this represents racial discrimination,” he said.

That Judge Young would deliver such a frank ruling was perhaps unsurprising. His long career — President Ronald Reagan appointed him in 1985 — has been punctuated by high-profile cases and outspoken advocacy for the value and fact-finding power of the judiciary.