Rajesh was born in Kerala to a Malayali family. He inherited a flair for Kathakali, the classical dance of Kerala, from Siva Sankaran Nair, his father who was a veteran Kathakali artist. He also had some early training in Kalaripayattu, the martial art of Kerala. He took his Bachelor degree in Design and Direction from the School of Drama in Trissur, Kerala and directed more than 30 plays in Malayalam, English and Telugu. He worked with the National School of Drama, New Delhi as a designer in 1995. Rajesh won the Charles Wallace Trust Award and did his Masters in Visual Language/Scenography and Direction from the Wimbledon College of Art, London.

Rajesh's debut film In the Name of Buddha (2002) was premiered at the Oslo International Film Festival and won critical acclaim. The movie was nominated for the Best Debut Director category at the Cannes Film Festival. Though controversial in theme, the film is a non-partisan treatment of the ethnic conflict then raging in Sri Lanka with a hint of magic realism. The film was well received in many international film festivals in 2003 and won the Best Foreign Film award at the Beverly Hills International Film Festival, the Newport Beach International Film Festival and at the Wine Country International Film Festival in the same year.
Following the success of In the Name of Buddha, Rajesh directed the music video for "Sunshowers" for Maya Arulpragasam (M.I.A.). She is known for her "O Saya" with A.R. Rahman for Slumdog Millionaire which was nominated for the Oscars in 2009. Rajesh directed Ente Malayalam, a promotion for the Manorama Music channel to celebrate the 50th year of Kerala formation, capturing noted Malayali achievers against the lush landscape of Kerala in evocative frames.
Rajesh directed two Telugu films in the interim: 10 the Strangers and Alex, the Blue Fox. Besides feature films and music albums/videos, he has essayed other genres including documentaries, short films, ad films, public service announcements and commercials and won many accolades.