Mass General Brigham attributed the layoffs to an expected budget shortfall of $250 billion over the next two years.

Its flagship academic medical centers in Boston, Massachusetts General Hospital and Brigham and Women’s Hospital, anchor a health care hub that is arguably the best in the country, if not the world.

The Mass General Brigham CEO received a hefty 40% raise, the latest available tax records show, with the hospital system now saying it must roll out mass layoffs to quell a looming budget deficit.

Last year, Massachusetts General Hospital announced it was adding 94 beds as some patients are left waiting for days in the Emergency Department for a hospital bed. In recent years the health care ...