Harbour Church will be aimed specifically at students and young adults, and will hold its first service this Sunday.
The congregation will be made up of 30 worshippers who have relocated to the city from St Peter's Church, Brighton, taking up new jobs or university courses.
They hope to grow to more than 200 within five years.
The new church is part of the Dioecese of Portsmouth's strategy to grow numerically and spiritually by 2021.
Plans for the church include supporting the homeless, those in debt and the unemployed in the city. A new coffee shop will be opened which will also create jobs.
Bishop of Portsmouth, Rt Rev Christopher Foster, will be at Harbour Church for the launch where worshippers will enjoy bacon sandwiches and bucks fizz.
He said: "I am a fervent believer in the importance of traditional parish ministry and chaplaincy. There are some fantastic examples in our diocese of congregations that are vibrant and often growing because they are sharing God's love effectively with others.
"But I also know that we have to find new ways to create disciples among those we have often found hardest to reach, such as inner-city estates, new areas of housing and with younger people.
"A key part of our strategy is pioneering ministry and fresh expressions of worship - finding ways of reaching out to those who simply aren't interested in our traditional models of church."