The meeting comes a day after the national executive meeting of BJP concluded here.
BJP sources described the meeting as a courtesy call by Gadkari.
The BJP chief had also met Thackeray last month, in an apparent effort to remove the "misunderstanding" that had crept into their relations a few months ago over the BJP president not being able to reach out to the Sena chief over telephone.
During an interview given to a regional channel prior to civic elections, Thackeray had said that he had enjoyed excellent relations with Vajpayee and Advani, but did not jell well with the second generation of BJP leaders, including Gadkari.
On his part, Gadkari in an interview had lamented that he was unable to reach out to the Sena chief over phone, as the connection was not passed onto Thackeray at 'Matoshree'.