Edmund Lilly D.D. (died 7 February 1610) was an English academic administrator at the University of Oxford.
Lilly became Master (head) of Balliol College, Oxford on 1 August 1580, a post he held until his death in 1610. During his time as Master of Balliol, he was twice Vice-Chancellor of Oxford University for the periods 1585âÂÂ1586 and 1593âÂÂ1596. Lilly was deemed an "excellent divine".