The figure rose to TL79.5 million ($27.1 million) from TL37 million in the same period last year.
For the first half, the operating loss totalled TL285 million, up from TL48 million in the six months ended 30 June 2015.
Second-quarter revenue declined from TL834 million to TL798 million, but across the first half sales were up 5% at TL1.49 billion.
In the first seven months of the year, the airline adds, passenger numbers rose 8.8% to reach 13.46 million, of whom 4.84 million were travelling on international routes.
Pegasus chief executive Mehmet Nane says: "Despite the challenging conditions the tourism sector has experienced in 2016, we at Pegasusnever wavered from our growth targets or the belief in our country, working harder than ever to ensure that, despite the fall in demand on some of our routes, we achieved robust growth in our key target areas including for overall guest numbers, number of flights and turnover.
"Our results are even more significant given the backdrop of the issues our sector has faced in the first half of the year."