This is the first time that the carrier has posted a quarterly loss since getting listed in November 2015.
IndiGo, the country's largest airline with over 40 per cent market share, had a profit of Rs 5.51 billion in the same quarter a year-ago earlier.
According to a regulatory filing, IndiGo's total income rose over 18 per cent to Rs 65.14 billion in the second quarter ended September 2018.
In the same period a year ago, the total income stood at Rs 55.05 billion.
"High fuel cost, rupee depreciation and intense competition significantly impacted profitability," the filing said.
In the latest quarter under review, total expenses jumped 58.2 per cent to Rs 75.02 billion.
IndiGo's co-founder and interim CEO Rahul Bhatia said aviation in India is facing significant pressures from high fuel costs, rupee depreciation and intense competition, all of which have impacted the airline's profitability.
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