The 86th Fife group, based at Abbotshall Parish Church, have been given indications that they will have to find a new home as early as next year.
As well as this, the 80th Fife, based at Linktown Church on Nicol Street also faces an uncertain future due to the Kirk plans.
While the number of youngsters enjoying Scouting in Kirkcaldy is still growing, many other groups in the area are also facing difficulties in recruiting more adults to help out.
Although the Church of Scotland (CoS) says no decision has been made, the 86th have been told by the Abbotshall that they could be homeless as early as the first quarter of next year.
Jane McGuire, Group Scout Leader at 86th Fife, said: “It's devastating that we need to find a new home. We have around 65 kids from the age of 6 through to 17.
"There are other groups in Kirkcaldy, but we don’t know if they have space to take on any more youngsters, and are they local enough for our kids? Not everyone has a car.
“We’re considering other options, but it’s not very easy to find a place that can house us.
“Scout groups come with a lot of tents and all manner of camping equipment.
“We have potentially less than 6 months. It's quite scary.
"If we can't find a home then there's potentially no troop.”
She said the loss of the group would deprive many youngsters in the area a valuable resource.
She added: “They get to experience things they never otherwise would, like camping and all other outdoor pursuits.
“We’ve had kids in the past who have had a rough time elsewhere in life and Scouting is their space on a Friday night to just be kids, free of bullying or whatever else they may have going on. Scouting is a great thing to be involved in.
"It's such a shame that the group might have to disband due to this situation and we'd appreciate any help we can get."
Rob Sutherland, Group Scout Leader of the 80th Fife said the group only recently found out that Linktown Church was among those earmarked for closure.
Rob said: "It came as a surprise to Linktown Church.
"We are uncertain as to when it'll happen.
“We're providing skills for life. We give kids the opportunity to explore the world around them and to learn about the outdoors in a safe manner.
“We have a very mixed demographic and we make Scouting accessible to everyone in the Linktown area.
“If we lose the church, that leaves two Scout troops at the west side of Kirkcaldy homeless.”
A spokesman for the Church of Scotland said: “There are currently four church buildings in Kirkcaldy town centre and it is no longer financially sustainable to maintain them all.
“It has been proposed that the number is reduced to two.
“Fife Presbytery recognises that Abbotshall Church and Linktown Church have significance and meaning to those who have met and worshipped there and the groups who use the buildings.
“Church members in Kirkcaldy are willing to hold discussions with groups to help them identify suitable, alternative arrangements elsewhere in the town.
“No final decisions have been taken by Fife Presbytery and it is proposed that buildings classified as being no longer fit for purpose will be sold sometime within the five-year lifetime of an approved plan”.