Asin was born in Cochin (now Kochi) in Kerala on 26 October 1985, to a Syro-Malabar Catholic Nasrani family. Her father, Joseph Thottumkal originally from Thodupuzha, managed several businesses. Her mother, Seline Thottumkal, is a surgeon. Asin is their only child. Asin's father was keen to name her as Mary, after her grandmother. He however named her Asin as the name had a beautiful meaning. Asin has quoted that her name means "pure and without blemish". She states that the 'A' in her name is from Sanskrit meaning "without", and 'sin' from English".

Asin attended Naval Public School from LKG through X standard. She scored over 90% in her X board exams but chose Humanities in XI standard, shocking her family who were confident she would take up science and get into the civil services. She then attended St. Teresa's School in Kochi for her Plus Two education. After that she attended St. Teresa's College in Kochi, a college affiliated with MG University, where she graduated with a Bachelors of Arts degree in English Literature. The actress can speak seven languages; being well-versed in Malayalam (her mother tongue), Tamil, Telugu, Hindi, French, English and Sanskrit.