The airline posted a net loss of 3.84 billion rupees (80 million dollars) after announcing a profit of 283.
6 million rupees a year earlier.
"The company suffered losses mainly on account of high fuel and lower load factors, resulting in lower-than-expected revenues," Jet executive director Saroj Dutta said in a statement.
Revenues for the July-September quarter rose 45 percent to 32.58 billion rupees for the airline which flies domestic and international routes and has a budget carrier named JetLite.
India's crowded airline sector posted a combined loss of 938 million dollars last year and analysts expect the figure to more than double this year.
Earlier this month Jet struck an alliance with fierce rival Kingfisher Airlines to help both carriers battle slowing passenger growth and high fuel costs which have pushed up fares.
The Jet-Kingfisher alliance involves joint fuel management, ground handling, network rationalisation and crew sharing.
However, both the airlines wil