He took the Metro to avoid inconvenience to the public on the route because of the security arrangements, sources said.
The prime minister was to attend a function of the National Intelligence Academy.
When the prime minister travels, the road is closed for sometime for his movement.
Modi said he really enjoyed the Metro ride.
"Sreedharanji would always tell me to experience the Delhi Metro. Today I had the opportunity to do so on the way to Dwarka," he tweeted.
"Really enjoyed the ride. Thanks Delhi Metro. Thanks Sreedharanji!," he said.
E Sreedharan is the former chief of Delhi Metro Rail Corporation and is popularly known as 'Metro man'.
Modi was accompanied by National Security Advisor Ajit Doval.