The NYPD’s highest-paid employee — who shoveled in more than $400,000 last year — filed for retirement this week and then was suspended amid an internal affairs probe into her astronomical overtime, The Post has learned.

Lt. Quathisha Epps will retire just shy of 20 years with the department, sources said — an early exit that will impact her pension and cost her a $12,000-a-year supplement for cops who reach the two-decade mark.

Leaving money on the table is seemingly uncharacteristic for Epps, who raised eyebrows by pulling in roughly $204,000 in overtime last year for her administrative job in NYPD Chief of Department Jeffrey Maddrey’s office, payroll records show.

Sources told The Post that Epps’ whopping overtime was capped after The Post’s exclusive report last month on her pay. She was also told she’d be put back on patrol — an apparently unappetizing prospect after her cushy desk job, according to the sources.

“There is no way she was going to go out on patrol,” one source told The Post.