Dilip D'Souza was born to Neela, a Tamilian and former Maharashtra Chief Secretary and activist J.B. D'Souza. D'Souza did a BE in Electrical and Electronics Engineering from BITS Pilani (1976–81) and an MS in Computer Science from Brown University (1984).

He married French language teacher Vibha Kamat in 1993, and they have two children, son Sahir, born 1999 and daughter Surabhi, born 2004. He studied and worked as a software engineer in United States from 1981 to 1992 when he returned to India to write full-time.[8] He speaks Tamil, Hindi, Marathi, konkani, English, French and Spanish.

As an alumnus of Birla Institute of Technology and Science, he is dedicated to alumni activities and has come over many times to his alma mater. He was there in February 2010 to promote his new book Roadrunner. He is currently on the editorial board of the BITS Alumni magazine Sandpaper. D'Souza also maintains a blog "Death Ends Fun"