The flight IX-662, with 182 passengers, was operated in recognition of Captain Krottapalli's feat in becoming the first commander of the airlines.
Speaking to reporters before flying to Singapore, she said, "I feel very proud of this moment".
A native of Andhra Pradesh, Krottapalli joined Air India Express in November 2004.
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The cabin crew comprised S Banu, P Bhutia, S Divya and Binal Valand.
Air India Express currently has a total of 76 pilots, of which only six are women pilots.