The duo met at a hotel in the evening where state Chief Secretary Basudeb Banerjee was also present.
Tobgay is in the city at the invitation of the state government to attend the two-day Bengal Global Business Summit beginning on January 8.
Last October, Mamata Banerjee had gone on a five-day tour to Bhutan during which she had invited Tobgay.
The Bhutanese PM had developed a good rapport with Banerjee and even drove her once to the hotel in Thimphu.