It was dubbed a deal between atheists and theists over allowing prayers in schools to be debated by Members of the Scottish Parliament.
The church and the humanists jointly called for legislation to change "Religious Observance" in Scottish school assemblies to "Time for Reflection."
The aim is to make these events inclusive of as many pupils as possibly, and "clearly not gatherings where one faith or belief system is promoted over another," says a press release from the two bodies.
The Christian think tank Ekklesia said, "The agreement in principle on an issue which has stoked heated debate marks a significant breakthrough - and a joint statement by the Kirk and a body seeking to give voice to ethical non-believers appears to be a first."
The Church of Scotland, known informally by its Scots name, the Kirk, is the biggest church in the country claiming the allegiance of around 32 percent of Scotland's five million people.
Around 16 percent of Scots are recorded as Roman Catholics while 1.4 percent, are followers of Islam.
SCOTLAND'S NATIONAL CHURCH
The Kirk is Scotland's national church and its identity was decisively shaped by the Scottish Reformation.
The Humanist Society states it aims to promote a secular Scotland through its work in policy, in education and its range of ceremonies.
The 2011 census shows that 37 percent of the people in Scotland claim no religious affiliation.
Scottish debate has revolved around issues of parental and pupil choice, the extent to which they are confessional or informational, and the scope of the reflections and practices involved regarding Religious Observance.
Debate has also centered on whether the current system offers a range of viewpoints in line with the demography of the country.
When the Church of Scotland puts its views forward on "Time for Reflection" in October, Free Church minister and director of the Solas Centre for Public Christianity, Rev. David Robertson, accused the Kirk of "capitulating to the secularist agenda."
"Without Christian worship, Christianity does not exist.
"When the Church says it does not want worship or prayers but instead advocates what will inevitably be a State-sponsored non-Christian moralism, it has reached the stage where it is no longer fit for purpose and should no longer seek to style itself as Scotland's national Christian church," said Davidson.
Rev. Sally Foster-Fulton, convener of the church and society council of the Church of Scotland, said, "We welcome this exciting opportunity to collaborate with our humanist colleagues in supporting genuinely inclusive Time for Reflection.
She said the viewpoint "supports the community and spiritual development of all pupils whatever their faith or belief."
She noted, "Scotland is a wonderfully diverse nation. Regular, inclusive Time for Reflection will enhance young people's ability to celebrate difference rooted in respect."
Douglas McLellan, chief executive of the Humanist Society Scotland said, "We welcome the opportunity to work collaboratively with the Kirk. We urge the Public Petitions Committee to make strong recommendations for the change of Religious Observance to 'Time for Reflection.'
"This removes the religious exclusivity of the current system and brings about fairness and equality for all. If this change is made, it will bring current practices in-line with the modern demographic in Scotland," he said.
The Church of Scotland and the Humanist Society Scotland will make their joint submission to Public Petitions Committee of the Scottish Government on January 28.
There also be discussion on another petition, from the Scottish Secular Society calling basically for the removal of religious observance.
The Kirk and the humanists will urge the Scottish Government bring forward legislative proposals to remove the reference to "Religious Observance" in the Education (Scotland) Act 1980 and insert "Time for Reflection" instead.
'SHARE PUBLIC SPACE'
Simon Barrow, co-director to Christian think tank Ekklesia said, "It is vital for a healthy society that people of different religious and non-religious outlooks can learn to share public space fairly, collaborate on common values, uphold the rights and dignity of all, and negotiate disagreements with informed respect."
Ekklesia, which examines the changing place of belief in the contemporary world, argues that, in a plural society, religions should neither be established nor excluded.
"A 'Time of Reflection' in schools ought to be a space where these virtues can be put into practice by breaking down barriers, challenging prejudices and providing opportunities for the appreciation of different viewpoints and experiences.
"The Kirk and the Humanist Society are right that such vital space for reflection in schools should not be restricted on grounds of religion or belief. A genuinely multi-voiced education system is to the benefit of all," said Barrow.
The Church of Scotland has suggested a number of principles for the practice of "Time of Reflection."
Among these are that Head teachers decide who leads it; outside leaders, including chaplains, do so to assist the school in delivering a "Time for Reflection" agenda defined by the school, bound by the need to be genuinely inclusive.
It should never be confessional in nature nor worship or State sponsored prayers; and the best "Time for Reflections" are often pupil led.
The Scottish Secular Society said it would back legislative change, but noted, "The suggested change in terminology would in and of itself do nothing to prevent the abuses that we reported in our petition and earlier related evidence.
"In addition, it runs the risk of adding to the existing confusion already experienced by parents over what their children are taught in this area."