Now, world leaders are scrambling to prevent a fourth amid rising tensions between the two countries.
India and Pakistan - both nuclear powers - claim all of Kashmir, but each controls only parts of it.
Varthaman was arrested by the Pakistani army on Wednesday, when his fighter jet was hit by a Pakistani missile across the Line of Control in Kashmir and he ejected in the enemy country.
Tensions escalated between Islamabad and New Delhi following a suicide attack on Indian security personnel in Indian-controlled Kashmir on February 14, which killed over 40 paramilitary troopers.
In a separate interview to BBC News, the foreign minister, in response to a question pertaining to the Pulwama incident, said that there was "still confusion" over whether the Jaish-e-Mohammad (JeM) group had claimed responsibility for the attack or not.
The pilot himself thanked the Pakistani army for how he had been treated in a speech broadcasted by Islamabad's national TV.
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Prime Minister Narendra Modi welcomed the return of Varthaman, saying the nation is proud of his exemplary courage. They have fought three wars, two directly dealing with the disputed region.
The IAF pilot, defence forces said, shot down the jet which was on a mission to attack Indian military base.
On Wednesday he pushed for talks with Delhi to prevent the risk of a "miscalculation" between the nuclear-armed neighbours. Pakistan had acquired the F-16 fighter jets from USA to "fight against terrorism" in 2008. Tonight on Left Right and Centre we ask, is Abhinandan's return enough for de-escalation or is this just a temporary hiatus.
Two Indian air force jets then responded, crossing the de facto border that divides Kashmir.
Indian pilot, Wing Commander Abhinandan, stands under armed escort near Pakistan-India border in Wagah, Pakistan in this March 1, 2019 image from a video footage. Going forward, Indian officials said they would strike targets, including those inside Pakistani territory, if officials receive intelligence of planned attacks.
Before the pilot was released, Pakistani television stations broadcast video of him, looking cleaned up and thanking the Pakistani Army for treating him well.
The hostage crisis lasted several days, with Indian authorities agreeing to release Azhar after the hijackers slit a passenger's throat and threatened to kill more.
The pilot's family have not yet commented on the events.