The budget airline will operate 14 weekly flights from the airport to Bucharest and Sibiu in Romania and Vilnius in Lithuania.
The new routes, which will start in October and November, are part of a five-year partnership signed between Stobart and Wizz Air.
Stobart said the routes are expected to bring in 250,000 passengers in the first year of the deal, putting it on track to meet its target of five million passengers by February 2023.
"The agreement with Wizz Air is another significant milestone in the development of the UK's fastest-growing airport, London Southend Airport,” said chief executive Warwick Brady.
“The partnership increases the domestic and European destinations we can offer customers to more than 40 by adding exciting and increasingly popular destinations in Central and Eastern Europe.”
Last year Southend increased passenger numbers by one-third to 1.5mln and this year has seen “substantial progress”, CEO Brady said.
“Not only in terms of more airlines starting services, but the continued development of the airport's infrastructure and retail offering,” he added.
"These improvements include new early and late trains from London Liverpool Street and enhanced food and beverage options in the terminal, as we build towards our target of £8 EBITDA (earnings) per passenger."
Stobart pointed out that it takes just over 50 minutes for passengers to travel from London Liverpool Street Station to Southend and this easy access has attracted the likes of Wizz Air.
“The frequent train services have also helped increase the growth of the airport, which is now seeing more than 65% of its customers travelling from the Inner London area, and London Southend Airport's ease-of-use and customer service has seen consumer group Which? rank it the best London airport for five consecutive years,” Brady said.