The airline said it would continue to operate services between London and Hong Kong but the decision would affect some staff in Sydney and Hong Kong and it has started consultation with employees.
"Despite the best efforts of our employees, external factors such as increasing costs and a weakening Australian dollar have affected our profitability," Virgin Atlantic CEO Craig Kreeger said in a statement.
"These are still difficult times for the airline industry and as part of our strategy to operate more efficiently, we need to deploy our aircraft to routes with the right level of demand to be financially viable."
A company spokeswoman could not give any further details about the scale of job losses.
The airline said its last flight from Sydney to Hong Kong would be on May 5 and the last flight departing from Hong Kong to Sydney would be on May 4.