The pair are being medically examined under the assumption they are infected with the life-threatening Marburg virus, which can cause high fever, haemorrhaging and other symptoms close to Ebola, which is the same sort of virus.
The World Health Organisation says a high percentage of those infected with the Marburg virus have died in previous outbreaks.
According to Hamburg city council, one of the two people had recently worked in a hospital in Rwanda where people infected with the virus had been treated.
They developed flu-like symptoms on their way to Hamburg.
The pair were taken to hospital from the city's central railway station in a special "infection vehicle," a spokesman for the Hamburg fire brigade said.
A platform at the station was briefly closed during the operation but has since reopened.
The Marburg virus has no vaccine or antiviral treatment, the WHO says.
A west African outbreak of Ebola in 2013 led to more than 10,000 deaths over three years.
The Marburg virus can also cause muscle pain, abdominal cramps, diarrhoea and bloody vomiting.
According to the US health authority CDC, there has not been an outbreak of the disease in Germany since 1967.
The pathogen bears the name of the German city Marburg because laboratory employees there were infected with the previously unknown virus from experimental monkeys in 1967.
People become infected through direct contact with the body fluids of those infected, such as blood, but not through the air.Â
The incubation period is two to 21 days.
