Thirteen separatist politicians from the region have also been charged with the same and could face up to 30 years in prison under Spanish laws.
Supreme Court Judge Pablo Llarena issued the indictment on Friday, wrapping up a four-month long investigation into the events last autumn.
Catalan could face another regional election in two months after the separatist majority in its parliament failed to elect a president.
Puigdemont is currently living in self-imposed exile in Belgium and says the Spanish government has violated his rights to political freedom.
He faces arrest if he re-enters Spain.
Also charged with rebellion are Catalan vice president Oriol Junqueras, former Catalan parliament speaker Carme Forcadell, separatist activists Jordi Sanchez and Jordi Cuixart and ERC party leader Marta Rovira, who on Friday announced that she was fleeing Spain.