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

Saji Thomas worked for 14 years as an Evangelist and Pastor.  He worked for 5 years with Youth With A Mission in Chennai as an Administrator. He also Pioneered a new ministry in Kochi and worked there for 7 years. He also pioneered a ministry in Kampala, Uganda in 2013 and Luwero in 2020. After 10 years of his service in Uganda, he moved to Suriname in South America to pioneer a new project. In 1988 he did DTS with YWAM and in 1999, he did SOEP.

He married Sheena in 1990 and had two children Kesia born 6 June 1991 and Keran born 8 April 2003.

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