Saji Thomas was born and raised in a devoted Christian family in Kerala, India. His parents were upright Christians in the village. They brought their children up in discipline and Christian beliefs. After his Bible College in 1987, he started his mission work in different parts of India and Nepal.

He married Sheena in 1990, and they worked for 14 years as an Evangelist and Pastor. They worked for 5 years with Youth With A Mission in Chennai as an Administrator. After that, they pioneered a new ministry in Kochi and worked there for 7 years. They also pioneered a ministry in Kampala, Uganda, in 2013 and in Luwero in 2020. After 11 years of their service in Uganda, they moved to Suriname in South America to pioneer a new project. And now they are working in YWAM San Francisco.

In 1988, Saji Thomas did DTS with YWAM, and in 1999, he did SOEP.

They have two children: Kesia, born 6 June 1991, and Keran, born 8 April 2003. Kesia is married to Nelson, and they have three children.

His wife, Sheena, comes from a Marthomite family in Kerala. She did her DTS in 1998 in Chennai.