Arafat died eight years ago at age 75 in France of indeterminate causes after medical treatment outside Paris.
At the time, his widow, Suha, requested no autopsy be done. She has since given permission for the testing.
France ordered a new homicide investigation in August when traces of radioactive polonium were found on Arafat's clothing.
Palestinian and French officials will oversee the exhumation and take samples Tuesday, and the remains will then be reburied in the mausoleum in Ramallah with military honors, the Palestinian Ma'an news agency said.
The Palestinian ambassador to Russia, Faed Mustafa, said Russia will send forensic experts to examine the samples.
Arafat was confined to his compound in Ramallah for more than two years by Israel before he went to France for medical treatment, the Voice of America said.