"On Human Rights Day, my thoughts go to Fariba Adelkhah and Roland Marchal, our compatriots held in Iran, and their families," Macron said on Twitter.
"Their imprisonment is intolerable. They must be freed without delay. I told President Rouhani, I repeat it here," he wrote.
Marchal, a senior researcher at Science-Po university in Paris, and his Franco-Iranian colleague Adelkhah have been in prison in Iran since June, though French officials only went public about Marchal's detention in mid-October.
The arrests came as Macron conducts intense diplomacy to find a way of keeping alive the 2015 nuclear deal which limits Iran's atomic programme.
Iran has several dual nationals and Western passport holders in detention. Rights groups accuse Tehran of using them to extract concessions from Western countries.
They include British-Iranian Nazanin Zaghari-Ratcliffe, a project manager with the Thomson Reuters Foundation, who has been jailed in Tehran since 2016 on sedition charges, causing major tensions with Britain.