The leaders spoke for about an hour following two events that Harper attended earlier in Mississauga.
After the meeting, Tory said on his Twitter feed that his first sit down with Harper as mayor was "positive," and that they "spent considerable time talking about SmartTrack." Tory also said that jobs, the economy and housing were discussed as well.
Alleviating traffic congestion and streamlining the start of SmartTrack construction have been priorities for Tory since he formally took office Dec. 1.
Tory said earlier this week that his administration will aggressively seek more funding from the federal and provincial governments to tackle the city's most pressing issues, something that former mayor Rob Ford largely failed to accomplish despite a number of personal meetings with Harper during his time in office.
The meeting came on the same day that Ontario Premier Kathleen Wynne sent another letter to Harper — the latest in a series of letters to the prime minister — requesting a face-to-face discussion ahead of the federal government's next budget.
Harper said recently that the Ontario government should focus less on "confrontation" and more on getting its fiscal house in order.
Tory told the Toronto Sun that he did not discuss the ongoing tensions with Wynne with the prime minister.