The Baptist Times, which has been published weekly since 1855, is folding due to falling circulation and difficulties in selling advertising space.
Editor Mark Woods said the newspaper was not immune to commercial pressures on newspapers.
Chairman of the Board of Directors of the newspaper, Bill Johnston, said the paper had been forced to depend on a subsidy from the BUGB for a number of years.
However the trustees of the BUGB took the decision to cease financial support for the paper next spring.
In a statement, the BUGB said: "The directors have considered a number of business options for the paper but with profound regret now conclude that it must close."
The paper will bow out with a special edition in January celebrating its 156-year history and the contribution the paper has made to the life of the Baptist denomination and the wider Christian world.
Mr Woods said: "It has been a great privilege to serve as editor of The Baptist Times, and I would like to pay tribute to the talented and dedicated colleagues with whom I have worked over the years.
"However, we have not been immune to the commercial pressures on newspapers in general or to the effect of wider issues in church life.
"We accept our closure with sadness, but appreciate the care given to the decision and the pastoral care shown to the staff."
Jonathan Edwards, BUGB General Secretary, paid tribute to the paper in a statement.
"The Baptist Times has occupied a huge place in the life of our Union and its passing will be a matter of sadness to thousands of people. It was not only valued by Baptists in this country but also by many of our ecumenical and international partners, who often tell me of how much they appreciate it," he said.
"I want to place on record our deep gratitude as a denomination to the editors and staff who have served us with huge ability and devotion, and to The Baptist Times Directors who have supported them."
While the weekly print newspaper will cease to exist, The Baptist Times brand will live on in the form of a new online website that will offer the latest Baptist news, and feature a downloadable weekly news digest for individuals and churches to print off.
"The core vision of the new The Baptist Times website will be to offer fresh news of interest to our Baptist family on a daily basis," said Amanda Allchorn, Head of Communications at the BUGB.
"We will seek to maximise the use of social media alongside the online service to get discussions and comments going on a range of topics.
"Our prayer is that people in our churches will get excited and inspired about how Baptist people are engaging in mission and ministry across the UK and beyond through this new resource."