Varghese has Malayali origins from Pathanamthitta in Kerala. He is married to Julie Varghese, a policy expert with Atlantic Council and international affairs director known for her work in the field of healthcare, politics and elections. The couple has one son together.

maju varghese parents

Varghese has been vocal about his parents' origins on public platforms. He calls them "heroes" who "gave me a shot at an amazing life and a chance to chase every dream." The family immigrated to the US after his mother Saroja, who then worked with the Indian Air Force, shifted base in the 1970s. She further worked as a nurse in the US and since her retirement has taken to writing in Malayalam.