The maiden flight of the airline began on November 3, 2011.

The inaugural flight route starts from Batulicin to Banjarbaru.

As of February 22, 2022, Jhonlin Air Transport has only 3 aircraft fixed wing : The former fleet of Jhonlin Air Transport is The Hawker 900XP PK-JBH one of the two belonging to the company was involved in an accident in February 2013 while landing at Halim airport in Jakarta.

The aircraft lost the left landing gear on impact.

[5] A Cessna Grand Caravan 208-EX PK-JBR also crashed in Papua in October 2018 carrying a passenger named Daus in Beoga, Puncak Regency in Papua.