Operations at all nine airports that were shut for civilian traffic, have resumed as of now, the DGCA said.
Earlier, the entire airspace north of the Indian capital was vacated, official sources said on Wednesday.
The skies above New Delhi were vacated as nine airports in Jammu and Kashmir, Himachal Pradesh and Punjab were closed for civilian air traffic on a day of rapidly escalating tensions between India and Pakistan.
National Security Advisor Ajit Doval held a high level meeting to assess the security situation in the wake of the developments of the morning, including Pakistan claiming that it had shot down two Indian military jets and arrested two pilots.
India said Pakistan jets intruded into the Indian air space in Rajouri and Poonch sectors.
The decision to stop flights to these airports came less than 24 hours after India launched what the government called a "non-military pre-emptive air strike" on one of the biggest training camps of terror group Jaish-e-Mohammed in Balakot in Pakistan on Tuesday.
While there was no official communication on why this was done, aviation industry sources claimed the move was taken as an Indian Air Force aircraft had crashed, leading to closure of civilian flights to these airports.