The airport resides at an elevation of above mean sea level. It has one asphalt paved runway designated 06/24 which measures. There is a down slope of 1.75% up to about from the threshold of runway 06. There is a terminal building for passengers. There are daily flights between Pokhara Airport and Jomsom during daylight hours in good weather. Although the flying distance is short and flight time just 20 minutes, very high mountains between Pokhara and Jomsom, including Dhaulagiri and Tukuche on the west and Nilgiri Central and Annapurna on the east, require planes to fly through the Kali Gandaki River gorge. With Jomsom Airport located at the head of the gorge, high terrain surrounding the airport presents a hazard when a go-around is required and when, as is frequently necessary after mid-morning, a turn is required at Jomsom to land into southerly winds. Heat from the sun in the Mustang District causes strong southerly winds in the Kali Gandaki River gorge and at Jomsom after early morning. Cloud cover, changing visibility, and high winds, often mean flights are delayed or the airport closed. The airport is available throughout the year but visibility is not adequate for visual flight rules flight about 15% of the time. As wind speeds increase during and the day and high wind speeds often prevent airport operation after midday, airlines schedule flights to Jomsom for the early morning when wind speeds are low. Airlines operate a shuttle service between Jomsom and Pokhara and planes are turned around as rapidly as possible at each airport in order to complete as many flights as possible before wind speeds at Jomsom become too high or visibility forces the suspension of flights.
On 21 August 1998, a Lumbini Airways de Havilland Canada DHC-6 Twin Otter leased from the Air Transport Support Centre on a late morning scheduled passenger flight from Jomsom to Pokhara impacted Mount Annapurna near Ghorepani at the 7000 ft level. All 18 occupants, three crew and 15 passengers, were killed and the plane damaged beyond repair.
On 14 May 2012, Agni Air Flight CHTDornier 228, a scheduled passenger flight from Pokhara to Jomsom, crashed into the side of a hill near Marpha village 5 km southwest of Jomsom Airport killing 15 of 21 people on board. The flight attendant and five of the eighteen passengers survived but the plane was damaged beyond repair. The crash claimed the life of Indian child actressTaruni Sachdev. The head of Nepal's national rescue department reported that the pilot told air traffic control moments before the crash that he was diverting back to Pokhara.
On 16 May 2013, Nepal Airlines Flight 555de Havilland DHC-6 Twin Otter, a scheduled passenger flight from Pokhara to Jomsom carrying 18 adult passengers, one infant, and three crew, crashed while landing at Jomsom at 8:30 AM and fell onto the bank of the Kali Gandaki River. The plane was extensively damaged. There were no fatalities but three people, two crew and one passenger, sustained serious injuries and one crew and six passengers sustained minor injuries. Eight of the plane's passengers were Japanese tourists while the three crew members and remaining passengers were Nepali. The final report found that the plane landed at excessive speed and too far from the runway threshold in the opposite direction to the notified direction in use with an eight to twelve knot tailwind. The aircraft departed the runway to the right side during braking, re-entered the runway under power at speed, and attempted to take off for a go-around with the flaps retracted. With insufficient speed and lift, the takeoff attempt failed and the aircraft overran the runway, breached the perimeter fence, and fell into the river. The Investigation identified inappropriate actions of the aircraft commander in respect of both the initial landing and his response to the subsequent runway excursion and also cited the absence of effective Crew Resource Management.
On 24 February 2016, Tara Air Flight 193, a Viking Air DHC-6-400 Twin Otter with registration 9N-AHH, a scheduled domestic passenger flight with 23 people onboard departing from Pokhara at 07:50 am for Jomsom went missing eight minutes after takeoff. Three helicopters dispatched to search for the missing aircraft were initially hampered by bad weather. Hours later, the wreckage and several charred bodies were found. There were no survivors. The crash was the twenty-second loss of a DHC-6 in Nepal, the seventh-deadliest aircraft crash in Nepal, and the world's fourth-deadliest accident involving a DHC-6. It was found that en route, flying under visual flight rules, the flight had deviated to the left and climbed to to avoid clouds before beginning a descent to after entering cloud. The captain initiated another climb one minute before impact shortly after the ground proximity warning system sounded at. Flying in cloud with little visibility the plane struck a mountainside at and came to a rest at near Dana village, Myagdi district.
