After arriving in Karachi, he was driven away under tight security from the Jinnah International Airport to the Bilawal House residence here.
Bilawal, 26, is expected to tour Punjab to address rallies in a bid to revive the party's fortunes ahead of local government elections later this year.
He had left the country last year when reports of differences with his father surfaced and he criticised the Muttahida Qaumi Movement party which soured the relationship between the two parties.
Bilawal is son of two-time Pakistan premier Benazir Bhutto who was killed in an attack in 2007.
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He was named as PPP chief by Benazir in a will revealed after her death.
But, in affect, the party has been led by Zardari who is known as the master of political manoeuvring.
Bilawal wants more effective control over the party affairs but Zardari is trying to gradually hand over the reins of the party to him.