The Rt Rev John Chalmers said the Church needs to be both accessible and relevant, but cautioned that time is not on its side.
He also looked ahead to a time when the issue of human sexuality - which has been high on the Kirk's agenda for several years - can be set aside and the Church can focus on its "urgent business".
The Moderator issued his urgent rallying call in an address to the General Assembly on the final day of the Kirk's annual gathering in Edinburgh.
He told commissioners: "We have heard some worrying facts this week. Facts that we cannot turn a blind eye to: a quarter of our charges do not have an inducted minister; we only have two ministers under the age of 30... (and) four times the number of ministers will retire in the next six years than we are likely to recruit in the same time-frame.
"A tide has to be turned because a generation of people out there are being invited to live a life of disbelief - if not unbelief. And there is no justification for that.
"This Church of ours has to stop its navel gazing, get out from under subjects that no one is actually talking about and get out there and capitalise on the fact that people still want purpose and faith in their lives.
"They just need it to be accessible, relevant, generous, forgiving. Actually they need it to be like Jesus: accessible, relevant, generous, forgiving.
"But let me tell you, we don't have time on our side."
He described this year's General Assembly as a "momentous week" for the Church and said its debate on the independence referendum was an "important contribution to the discussion about Scotland's future".
Mr Chalmers also referred to the long-running debate on the role of gay ministers within the Church.
Earlier this week, the Church voted in favour of a proposal which could lead to the ordination of ministers in civil partnerships. The issue has now been sent to presbyteries for further discussion.
Mr Chalmers told the Assembly: "We have dealt with our own internal struggles and we have sent to our presbyteries an overture which may pave the way for a period of Church life when we will set the issue of human sexuality to one side and focus on the urgent business of mission, ministry and service to the people of Scotland."