At 18, Mazari got married. Her then-husband was a pilot called Khurram Shahzad, and he worked in the Pakistani Air-force. However, their relationship was short-lived. In 2014, Muniba and her husband separated, and a divorce followed in 2015. Her ex-husband took her to court two years later, suing her for defamation. He wanted 10 Million Pakistani Rupees as compensation. Nonetheless, the case was dismissed in January 2018 by the court. Muniba has an adorable son called Nael. She adopted him in 2011.