Both cases are of rape and murder of a 4-year-old girl by three men in Indore in 2012, and of a 22-year-old woman by two men in Pune in 2007.
The two pleas were received in the President's secretariat in April and May.
The convicts had urged the President to commute the death penalty awarded to them by local courts concerned and upheld by respective high courts and finally by the Supreme Court.
In the gruesome rape and murder case of Indore, Jitendra alias Jeetu, Babu alias Ketan and Sanni alias Devendra were handed down death sentence by a city court a year after the crime was committed.
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Mukherjee rejected their mercy petition on May 25, a Rashtrapati Bhavan communique said.
The convicts had kidnapped the child from outside her relative's house in Nehru Nagar area of Indore. They then sexually assaulted, strangled her to death and dumped the body in a drain.
In the Pune case, the convicts -- cab driver Purushottam Dashrath Borate and his accomplice Pradeep Yeshwant Kokade -- had raped and murdered the woman.
The woman, who was on her way to office for a night shift, was picked up by the cab. She was abducted, raped and killed by the driver and his aide -- the two convicts.
Their mercy petition was rejected by the president on May 26.
With these two cases, the total number of mercy petitions rejected by Mukherjee during his tenure has gone up to 30.
As per rules, there is no fixed time limit for the president to decide on a mercy petition.
President Pranab Mukherjee completes his five-year tenure on July 24.