The city borders Hong Kong, which has culled thousands of chickens and ordered a suspension of live poultry imports from China after three birds tested positive with the strain in mid-December.
The man, a bus driver surnamed Chen, was hospitalised with a fever on December 21 and tested positive for the H5N1 avian influenza virus in Shenzhen's Bao'an district, the provincial health department said, according to Xinhua news agency.
He remains in a critical condition and is receiving emergency treatment, the report said, adding that the man had apparently had no direct contact with poultry in the month before he was taken ill nor had he left the city.
Chinese and Hong Kong authorities have been working closely together since December 21 after live poultry supplies were suspended to the glitzy financial hub following the discovery of infected birds.
Chinese health authorities vowed to stay in "close contact and work together" with Hong Kong and "jointly step up measures in controlling the epidemic", the report said.
Authorities in Hong Kong raised the bird flu alert level to "serious" as they tried to trace the origin of an infected chicken, resulting in major disruptions to poultry supplies over the busy Christmas period.
Two schools were ordered to close after dead birds infected with the virus were found on their premises.
Hong Kong was the site of the world's first major outbreak of bird flu among humans in 1997, when six people died. Millions of birds were then culled.
The virus, which does not pass easily from human to human, has killed more than 330 people around the world, with Indonesia the worst-hit country. Most human infections are the result of direct contact with infected birds.
In people it can cause fever, coughing, a sore throat, pneumonia, respiratory disease and, in about 60 percent of cases, death.
Scientists fear H5N1 will mutate into a form readily transmissible between humans, with the potential to cause millions of deaths.
Hong Kong is particularly nervous about infectious diseases after an outbreak of deadly respiratory disease SARS in 2003 killed 300 people in the city and a further 500 worldwide.
A 59-year-old woman tested positive for bird flu in 2010 in Hong Kong's first human case of the illness since 2003.