Yuri Borisov had been in the role since July 2022, presiding over the crash landing of the Luna-25 probe in August 2023, Moscow's first lunar lander mission in almost 50 years.
He has been replaced with Dmitry Bakanov, a 39-year-old deputy transport minister and former head of a satellite company, the Kremlin said.
Putin's spokesman Dmitry Peskov said the move was part of a "rotation", adding: "The corporation needs to dynamically develop."
Borisov often had extravagant ideas to develop Russia's space programme, including putting a nuclear reactor on the Moon with China, but struggled to put them into action.
Once a space-faring pioneer, Moscow has grappled with a loss of scientific talent and erratic funding since the collapse of the USSR, causing it to lag behind competitors like the United States and China.
The Russian segment of the International Space Station has suffered three coolant leaks in just over two years, with Moscow signalling it aims to pull out of the project as early as 2028 and build its own orbital station.
Borisov warned in 2023 that most Russian equipment on the station was beyond its warranty and that the ISS as a whole was "approaching the finish line of its existence".
Roscosmos also struggled with corruption under Borisov's tenure.
Prosecutors in December 2023 charged the deputy director of Roscosmos and two other accomplices with embezzling some $4.5 million from the crisis-hit sector.
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