The head of the Chicago Public Schools’ beleaguered special education department is leaving the district after less than two years on the job, in an abrupt exit that caught advocates off guard on Tuesday.

Elizabeth Keenan’s departure was revealed by the Special School District of St. Louis County, which announced she’s been hired to take over that Missouri district as superintendent in July.

CPS officials later confirmed Keenan’s departure.

“Supporting the needs of diverse learners is a top priority for Chicago Public Schools, and we thank Dr. Keenan for her contributions to our students and schools, and wish her the best in her new role,” said Michael Passman, spokesman for CPS.

Keenan joined CPS’ Diverse Learner Supports and Services department in 2016 as deputy chief to Patrick Baccellieri, a career administrator with no specific special ed background or certification.

Keenan took over the $175,00-per-year post when Baccellieri — the pick of scandal-plagued ex-CPS Chief Forrest Claypool — left the job in August 2017.

Soon after, the Illinois State Board of Education began investigating sudden and unpopular changes to special education at CPS, changes they believed were illegal and “driven by budgetary concerns.”

An independent monitor was appointed, after the state probe ruled the 2016 overhaul delayed and denied services to needy students and uncovered significant problems with CPS’ electronic forms used to develop individual programs for kids in need of special services.

Christine Palmieri, one of the parents who brought the case to the state board, said Keenan’s exit came as a surprise, but offered a chance for the district to “clean house.”

Palmieri, of the Chicago Special Education Parent Advocacy Committee, criticized Keenan, saying “she never took accountability for any of the violations that happened — some were previous to her, some were under her watch.”

Keenan, who will earn $245,000 in her new position, couldn’t immediately be reached for comment.

“Special education is near and dear to my heart,” she was quoted as saying in the St. Louis County announcement. “While I ultimately wanted to serve as a school district superintendent, I didn’t want to lose that piece.”