A plane carrying Musharraf, leaders of his party and media persons from Dubai landed soon after noon at the port city of Karachi where supporters accorded him a warm welcome.
The authorities in Karachi cancelled permission for a Musharraf rally at the mausoleum of the founder of the nation over security concerns.
Musharraf had been living in exile in Britain and the United Arab Emirates since he resigned from his post in August 2008.
Musharraf, 69, had previously announced on several occasions that he would return home, but he had postponed the plan.
A court in Pakistan Friday granted protective bail to Musharraf, who had been facing arrest in several cases.
The 14-day-long protective bail was granted in response to a constitutional petition submitted to the court by Musharraf's daughter Ayla Raza Musharraf on behalf of her father.
An anti-terrorism court had issued arrest warrant in 2011 for Musharraf in connection with the murder of former prime minister Benazir Bhutto.
In October, a court also issued a warrant for his arrest over the killing of Baloch nationalist leader Akbar Bugti in a military operation in August 2006.
Musharraf, who ruled Pakistan from 1999 to 2008, has also been charged with ordering a military raid on the Taliban-linked Red Mosque in Islamabad during his term.
He dismissed all charges as politically-motivated and said in Dubai Saturday that he would defend himself in courts on return.
Pakistani Taliban Saturday issued a video, warning against his return, but he downplayed the threats and said he has been facing the dangers since 2001.
He also planned to run election campaign for his All Pakistan Muslim League party and to contest for a National Assembly seat in the May 11 election.
"My return is in the interest of Pakistan. The country's future is at stake and there is a need of a positive change in the country," Musharraf told a news conference in Dubai ahead of his return.