The two had an about 45-minute long meeting at Banerjee's Kalighat area residence.
Roy, a Rajya Sabha member, had last visited Banerjee's residence in February last year, just days after he was questioned by the CBI in Saradha scam.
"She is my chairperson and I am an MP of the party. I have been her soldier in several political battle. So there is nothing unnatural if I come to meet my leader," Roy said.
Asked what transpired in the meeting, he said, "We discussed a lot of issues."
He was stripped of party posts following his CBI quizzing in the multi-crore rupee scam.