The meeting lasted for nearly 30 minutes during which the National Conference leader briefed Mrs Gandhi about the political health of his state, official sources said in Delhi.
The meeting assumes significance amid loud cries in both the parties that they should not contest the forthcoming polls, scheduled later this year, together.
However, there was no official word from either parties about today's deliberations, the first after the Lok Sabha elections results were declared on May 16.
National Conference, which had four MPs in previous Lok Sabha, drew a blank in this year's parliamentary polls.
Congress, which had two MPs in previous Lok Sabha from the state, could not get a single seat.
While the opposition People's Democratic Part or PDP secured three Lok Sabha seats -- Srinagar, Anantnag and Baramulla -- from the Valley, the BJP walked away with the other three including its maiden victory in Ladakh.
Omar later met former prime minister Manmohan Singh.
"It was a pleasure to call on and spend some time talking to Manmohan Singh. I will always be grateful for his support and advice," he said.