Scott Waddell says his decision was voluntary but gave no reason for leaving as the BMV's commissioner.
Then-Gov. Mitch Daniels appointed Waddell to head the agency in October 2010 and Gov. Mike Pence decided to keep Waddell in place when he took office in January.
The BMV has faced lawsuits recently accusing it of overcharging fees and the agency announced last month it was cutting the fee for standard operator's licenses by $3.50.
Waddell's resignation statement cited improvements that have cut license branch visit times to less than 15 minutes and led to nearly half of all BMV transactions being completed outside a branch.