Markus Puusepp (born March 6, 1986 in Võru) is a former Estonian orienteering competitor and junior world champion.
He became Junior World Champion in the relay in Druskininkai in 2006, together with Mihkel Järveoja and Timo Sild.
He received a bronze medal in the long course at the same championship.
He competed at the 2009 World Orienteering Championships in Miskolc, Hungary.