Islam Siddiqui, 35, was hanged before dawn in central Pakistan's Multan prison, said jail superintendent Malik Ataullah on Saturday.
Siddiqui, a former soldier, was sentenced to death by a military court for involvement in a plot to kill Musharraf, who is also chief of the army staff, Ataullah said.
Musharraf survived two attempts on his life in December 2003 in Rawalpindi near the capital, Islamabad, when suspects with alleged links to al-Qaida tried to kill him with explosives for supporting the US-led "war on terror".
The president had rejected a mercy petition by Siddiqui, who came from the Jacobabad district of southern Sindh province.
Siddiqui's body was handed over to his family members for burial in his home town, Ataullah said.