Saqlain was born to a government clerk on 29 December, 1976, in Lahore. He has two elder brothers: Sibtain, who also played first-class cricket for Lahore, and Zulqurnain. Saqlain played for Govt. M. A. O College Lahore for three years and won the championship each year. Saqlain never played cricket at school level, but started playing for Zareef Memorial Cricket Club Second Eleven when he was only 13. He always wanted to be an off-spinner: "I never wanted to be a quick bowler. I was very skinny and never had too much strength in the body. " Saqlain was coached by Ahmad Hassan and his brothers at the club level. At the age of 14 he went to the Govt. M. A. O College Lahore, where he was coached by Mumtaz Akhtar Butt. He played for the college and won the championship for three consecutive years.