Having served within the organisation for 20 years he'll move from his current position as regional director for London & East.
He is also vicar of All Saints Woodford Wells in London.
He'll begin the role in October.
Speaking about the appointment, he said: "I am humbled and privileged to be taking on this role.
"New Wine has played a key role in my faith and in the life and growth of my church. I believe God is still using the network in powerful ways, and that there are greater things of the Kingdom to come in this nation.
"My prayer is that we will continue to push into his Spirit and follow his calling, to see churches across England be changed so that they can transform and bring renewal to community and culture.
"By continuing my role at All Saints, I intend to remain rooted in ministry within a local church that is part of a family of churches seeking to change nations."
His appointment comes just months after his predecessor Revd Mark Bailey stepped down over a disciplinary matter.
Speaking about the latest development, which comes a week before New Wine's summer festivals, its chair of trustees John Coles said: "After spending time in prayer and seeking the wisdom of those both within and outside the New Wine network, the New Wine Trustees are delighted that Paul has accepted our invitation to be our new National Leader.
"He brings with him a vast amount of experience leading a local church into renewal, and he is not afraid to trust the voice of God and take risks to advance the Kingdom.
"A strategic thinker who understands the vision and values of our network, Paul will bring a fresh leadership perspective to New Wine and is the right person to lead into the next season."
Between now and October, Revd Paul Harcourt will draw together a support team to help him move the organisation forward.
New Wine says this will be a diverse team in terms of age, gender, and geographical context.
Listen to Revd Paul Harcourt speaking to Premier's Aaron James on the News Hour: