The embattled head of the city agency that oversees the problem-plagued Superstorm Sandy rebuilding effort is resigning, Mayor Bill de Blasio announced Wednesday.

Feniosky Peña-Mora is stepping down as commissioner of the Department of Design and Construction to return to Columbia University as a professor. He previously served as a dean of the university’s Fu Foundation School of Engineering and Applied Science.

“I deeply appreciate Feniosky Peña-Mora’s extraordinary service to New York City,” the mayor said in a statement. “… While I am sorry to see him go, we did know this day would come. Indeed, he put off his return to Columbia, where he is a tenured professor, for an additional year to continue to serve the city.”

Peña-Mora, who is the latest in a long list of department heads to leave the de Blasio administration, announced his resignation following a NY1 report last week outlining many problems with the Sandy recovery program called “Build It Back.”

The program has been troubled by long delays, high costs and substandard work.

The storm struck in 2012.

A search is under way for Peña-Mora’s replacement.