The airport was shut at 10 p.m. local time (5 p.m. ET) and a 700-foot exclusion zone was set up to allow Royal Navy experts to safely remove the bomb. Local residents were also asked to leave their homes overnight.
A total of 284 flights were canceled Monday, affecting around 9,000 people, a spokesman for the airport told NBC News.
London was heavily bombarded during the Second World War and unexploded ordnance is regularly discovered, particularly during construction work.
London City Airport's runway was purpose-built on a marina adjacent to the Thames in 1987. A $477 million plan to expand the airport was approved in 2016.