His diploma film Genesis (1974), directed by Rahul Dasgupta, got many awards and started his career.

He became responsible with founder Chairman P R S Pillai, and its then Managing Director G.Vivekanandan for the planning, designing future visions of KSFDC to bring back the Film Industry that was until then rooted in Madras.

Since then after 30 years ,in 2024, the film by Ms Payal Kapadia from INDIA selected to compete for Cannes' Palme d'Or.

Then he continued working with notable directors like G. Aravindan, K. G. George and M. T. Vasudevan Nair as a cinematographer.

[4][5] His career also spreads to many activities by Government of India and Kerala where he served in the capacities of advisory status on policy decisions.

His latest film is titled Kutty Srank with Mammootty playing the lead role.

As of January 2018 Shaji is completing the post-production of a new movie titled Olu with Shane Nigam and Esther Anil playing the lead roles.

The film will attempt to convey her perception of innocent feminine desires – spiritual and transcendental feelings.

In May 2022 Shaji N Karun announced his next project based on the life of Amrita Sher-Gil, pioneer of Indian modern art.

In an interview with Jisha Surya of News9Live the cinematographer-director said that the multilingual movie will be based on the biographical writings of Sher-Gil.

Karun has approached a Mexican actor to play the lead role of the Hungarian-Indian painter.