Singh drove down to Rashtrapati Bhawan for a noon meeting with Mukherjee.
Officials described the meeting as a courtesy call.
This is the first meeting between Singh and Mukherjee since he assumed the office of President on Wednesday.
Vice President Hamid Ansari, Defence Minister A K Antony, Governors of several states, Leader of the Opposition in the Lok Sabha Sushma Swaraj were among those who had called on Mukherjee yesterday.