His resignation has been accepted by the Government, an official release said without assigning reason for Poonia's step.
Poonia was not contactable for comments on the matter.
HSTSB member Gyan Chand Sahota would now perform the duties of the Chairman till further orders.
Poonia, a close relative of Haryana CM Bhupinder Singh Hooda, was appointed as Chairman of the Board last year.
Poonia has been in the news including when Punjab and Haryana High Court had set aside the appointments of 1,983 Physical Training Instructors made by the state government last year.
The Court had also passed strictures against him, observing that the HSSC was nothing but "one man show" during the selections (of the Physical Training Instructors).