Bhoja Airline started its international operation on 24 January 1998 with a flight between Karachi and Dubai. Later, it started operating flights to the U.A.E from all major cities of Pakistan. In 2001, Bhoja Airline suspended its operations due to financial issues, although its airline license remained valid as issued by the Civil Aviation Authority, Pakistan.

After 11 years, the airline restarted their operations in the month of March, 2012. The airline started its operations with 3 aircrafts comprising 2 Boeing 737-200 and 1 Boeing 737-400. Reports indicate that the Boeing 737-400 is awaiting regulatory approval from the CAA.

On April 20, 2012 the airline started its first Karachi-Islamabad flight (Boeing 737-200) which unfortunately did not reach its destination. The Islamabad bound flight carrying 127 passengers crashed into a residential area 5 kilometers off the Chaklala airport. None of the passengers was able to survive the dreadful crash.