He got more votes than Amitabh Bachchan, who has a daughter and a son.
Shah Rukh Khan with wife Gauri Khan, son Aryan and daughter Suhana
The results of the poll, conducted among over 11,000 Indian women, by a matrimonial site, were announced a day ahead of Father's Day on Sunday.
Shah Rukh received 34.83 percent votes while Amitabh was chosen by 31.58 percent of the women surveyed. Cricketer Sachin Tendulkar took the third spot with 18.61 percent.
"The poll showcases some of the most successful Indian men whose love and dedication also makes them popular fathers. This suggests that people are looking at celebrities as real people with real relationships," said an official.
The poll also posed other questions to the respondents.
In the survey for the country's most popular father-daughter relationship, Big B took the top spot along with his daughter Shweta, who is married to businessman Nikhil Nanda.
Veteran actor Jeetendra and her film producer daughter Ekta Kapoor got 35.06 percent votes followed by father-daughter duo Anil Kapoor and Sonam Kapoor (22.42 percent).
Also, 44.85 percent Indian women voted for Shah Rukh and his son Aryan as India's most popular father-son duo.