Shea submitted paperwork last week an listed his final day on the job as Dec. 31.
The department's second in command -- First Deputy Commissioner Ben Tucker -- will also step down at the end of the year.
Tucker is the department's highest ranking Black member. He was appointed first deputy commissioner in 2014.
Shea had already publicly said he would leave the department at the end of the de Blasio administration.
The news comes a week after NYPD Chief of Department Rodney Harrison announced he would retire at the end of de Blasio's term as well.
Harrison is the only Member of the Service who has risen from the rank of Cadet to Chief of Department.
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