Jaan Tootsen (born October 14, 1975) is an Estonian film director, screenwriter and film producer.

Tootsen's father is journalist, writer and politician Toivo Tootsen. Since 2000 he has worked at Estonian National Broadcasting. He has been a long-time editor of radio program "Ööülikool". From 2012 to 2016 he was the cultural advisor for the Estonian president at the time Toomas Hendrik Ilves.