Modi arrived in Patna in the afternoon and drove straight to Mishra's residence.
"Modi visited Mishra's residence and paid his tributes," a BJP leader said.
Modi then met senior BJP leaders from Bihar, including Ravi Shankar Prasad, and flew back to Gujarat.
Earlier, Jharkhand chief minister Arjun Munda visited Mishra's residence.
BJP leaders LK Advani, Sushma Swaraj, Arun Jaitley and Ananth Kumar will attend Mishra's cremation in the evening.
Chief minister Nitish Kumar too visited Mishra's residence to pay his last respects.