The deaths occurred since late December after the patients contracted the virus, previously called swine flu, China Daily reported.
The report quoted the Beijing Centers for Disease Control and Prevention that despite its potential to cause harm, the virus is not as threatening and can be contained.
The report said both the victims of influenza A, or H1N1, virus were already in poor health when they were affected, said Pang Xinghuo, deputy director of the agency.
One of them was a 22-year-old suffering anemia, and the other a 65-year-old with terminal stage bone marrow cancer, Pang said, China Daily reported.
The virus caused panic across the world in 2009 as it spread. It killed at least 80 people in Beijing in 2009 and 2010, the report said.
Although flu viruses can pose a greater threat during the current unusually cold winter, Beijing health officials said its prevalence has been within expectations.
One official said in 2009, most people were very susceptible to the newly discovered virus, but since then many have developed immunity to it.