The meeting took place days after the BJP clinched a resounding victory in the civic and zilla parishad polls in the state.
Fadnavis, who led the BJP's campaign during these elections including that to the cash-rich Brihanmumbai Municipal Corporation (BMC), is learnt to have discussed with Modi the poll outcome and the issue of next Mumbai mayor during the nearly one-and-a-half hours meeting.
The BJP and its partner in central and state governments, the Shiv Sena, were locked in a bitter contest in the run up to the BMC polls.
The BJP, which made substantial gains from its previous tally of 31 seats, lagged behind the Shiv Sena by a slender margin of two seats.
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The NDA major had contested the Mumbai polls aiming to install its first mayor in the civic body, considered as the richest in Asia.
"The chief minister was in Delhi for the first time after the elections were held. He discussed the post-poll situation with Modi," a source said.
The chief minister parried questions on the possibility of the BJP and the Shiv Sena joining hands in the BMC, polls for which have thrown up a hung verdict.
"I will speak about Mumbai's issues in Mumbai only," he said.