Reddy, who landed at Begumpet Airport in a special aircraft from Vijayawada, reached the special court at Nampally Court Complex amid tight security.
This is the first time Reddy has personally appeared in the court as the chief minister in the case registered against him in 2011.
Reddy, who took over as the chief minister in May last year, has been seeking exemptions from personal appearance every Friday.
However, the special court, hearing Central Bureau of Investigation (CBI) cases, last week took exception to the YSR Congress Party (YSRCP) chief seeking exemptions every week.
Along with the chief minister, his close aide and YSR Congress MP V. Vijaya Sai Reddy, who is accused number two in the case, former minister and party leader Dharmana Prasad Rao, IAS officer Sri Laxmi, industrialist Shyamaprasad Reddy, retired IAS officer Samuel and other accused appeared before the court.
The court on November 1 last year had dismissed Jagan's petition for exemption from personal appearance in the case.
The chief minister had sought the exemption from personal appearance in the court on the ground that he is holding a constitutional post and needs to attend several important programmes.
However, the CBI had opposed the plea on the ground that there is a change only in personal capacity of the petitioner and not in the circumstances of the case. The federal agency had also argued that Jagan may influence the witnesses.
In what is known as ''quid-pro-quo'' cases, Jagan was accused of getting investments into his businesses by firms and individuals in return for the undue favours by the government headed by his father Y.S. Rajasekhara Reddy between 2004 and 2009. The CBI has filed 11 chargesheets against Jagan and others.
However, the YSRCP leader denied all the charges and termed them as political vendetta.
The CBI arrested Jagan and sent him to jail on May 27, 2012. After 16 months in jail, he was granted bail.
( With inputs from IANS )