According to state media, Mr Xi arrived in the city on Tuesday to inspect epidemic prevention and control work in the province.
Wuhan and its province, Hubei, have been on lockdown in order to prevent the spread of the disease. The president visited a community in the city currently in self-quarantine.
His visit comes as China records its lowest number of infections, just 19 on Tuesday, all in Wuhan apart from two who had arrived from overseas.
There have been 80,754 confirmed cases in mainland China and 3,136 people have died.
The visit was Mr Xi’s first trip to Wuhan since the outbreak began.
Global Times quoted analysts as saying Mr Xi’s visit sent a “strong signal to the entire country and the world that China is ascending out of the darkest moment amid the outbreak”.
The president also visited Huoshenshan Hospital, a temporary facility that was completed in 10 days. During his visit to the hospital, he learned about the facility’s operations, treatment of patients and protection for medical workers and scientific research there.
Images from his visit show the president speaking to staff and patients via video link.
Shortly after his visit, state media confirmed that all 14 of the temporary hospitals in China have now been closed.
It’s unclear how long Mr Xi will stay in the city.
Zhang Ming, a professor at Renmin University told Reuters news agency: “He is there now to reap the harvest. His being there means the Communist Party of China (CCP) may declare victory against the virus soon.”
In Qinghai province, the first batch of 144 senior schools and secondary vocational schools opened on Monday.
On Monday, Global Times said Tianhe Airport in Wuhan was preparing to reopen but no official date has been set.
Disneyland Shanghai says it has partially reopened. The main theme park is still closed but the shops and restaurants have reopened.