Opposing the central government's decision to carve out a separate Telangana state, he met the President at Rashtrapati Bhavan and submitted a five-page memorandum.
Jagan explained to Mukherjee the problems the bifurcation would lead to and requested him to ensure that the state remains united.
The YSRC leader explained to the President the problem of bifurcating the state
Jagan told reporters after the meeting that he conveyed to the President that the centre was trying to divide the state in an arbitrary manner.
He also told the president that this could set a bad precedent for division of other states.
The MP said the division would complicate the problem of river water sharing and would also affect the interests of government employees and students.
This was Jagan's second meeting with the president on the same issue. He had earlier called on Mukherjee when the latter had visited Hyderabad on November 4.
Meanwhile, the main opposition Telugu Desam Party (TDP) has found fault with the President giving an appointment to Jagan for the second time in less than 20 days.
TDP leader S Chandramohan Reddy said the first citizen's meeting with a man accused in a corruption case would send a wrong message to people.
Jagan, who spent nearly 16 months in jail was released on bail in September. A CBI court this week relaxed bail conditions to enable him to visit Delhi and other parts of the country.
The YSR Congress chief is visiting the national capital and other states to mobilise support from other parties to oppose Andhra Pradesh's bifurcation. He met Trinamool Congress leader and West Bengal Chief Minister Mamata Banerjee in Kolkata two days ago.
Jagan is scheduled to meet Janata Dal(United) chief Sharad Yadav in Delhi on Saturday evening. He will be visiting Bhubaneswar on Sunday to meet Biju Janta Dal leader and Odisha chief minister Naveen Patnaik.