The flight launches on January 7, 2019, and will be operated twice-daily on weekdays and once a day over the weekend.
In order to operate the route, the airline is leasing 4 new Embraer 190 jets while the route is expected to appeal to both the business-travel and city-break markets.
Adrian Kubicki, director corporate communications of LOT Polish Airlines, said: “We are extremely happy to announce this prestigious destination as our 100th connection in our network.
"LOT has a long lasting history of operations to London Heathrow, where we are flying three times a day.
"Now we are opening the new chapter by putting two daily flights to London City into our offer."
London City Airport chief commercial officer Richard Hill added: “A regular service between London City and Poland will now touch down with LOT Polish Airlines, boosting connectivity between London and Warsaw and adding another major European capital city to our route network.
"LOT’s arrival is a huge gain for London City Airport and its passengers, offering a gateway for trade and tourism in Central Europe and onward connections to Asia, and demonstrating the airport’s commitment to attracting new routes, greater choice and more airlines ahead of our £480 million development.
"It also demonstrates that, despite Brexit, London remains open for business and connections between Poland will continue to be vital for each country’s economy.”