Shaji is born to Shivaraman Nair who worked as an executive engineer in P.W.D & Janakiyamma on 15 August 1965. He got married to Annie on 1 June 1996 at the residence of his close friend Suresh Gopi, in the presence of a few close friends. Annie later adopted the name Chithra. Both fell in love with each other and got married. She had earlier acted in his film Rudraksham. They currently reside at Thiruvananthapuram and have three sons Jagan,Sharon & Rooshin. Jagan is in college, Sharon in 8th grade & Rooshin in 6th grade at Lecole Chempaka Trivandrum. His debut as a director was in 1989 with News, starring Suresh Gopi in the lead role. He got a break in the industry with the comedy film Dr. Pasupathy (1990). In 1994 Commissioner, (again with Suresh Gopi in title role) broke several box office records.
The year 2000 was a something special for Shaji Kailas as he brought out two huge hits in a row. Narasimham, released in the first weeks of the year, with Mohanlal in the lead role swept the box office. Scripted by Ranjith, this film was specially tailored for Mohanlal and succeeded in satisfying Lal fans and Narasimham completed 150 days in theatres. Just after the big success of Narasimham, again Shaji Kailas paired with Renjith, but this time it was Mammootty in the leading role. Valliettan, the Onam release of 2000 also successfully completed 150 days at box office. Following the huge success of these two films, Shaji made his debut in T Tamil film, with Vaanchinathan in (2001).