An expert in the mental wellbeing of young people, whose report identified the problem, suggests the economic downturn may be to blame for the phenomenon.
Recent years have seen a reversal of gains made in previous years, which had seen levels of happiness reported by young Scots rising steadily.
Katy Levin, senior researcher within public health for NHS Greater Glasgow and Clyde, said: "The happiness and confidence of young people in Scotland increased every four years, from 1992 to 2006, but dropped between 2006 and 2010. The rest of Scotland plateaued, but the reductions were so great in Glasgow this caused the whole of the country to fall.
"I would suggest this is because of the recession, which affected Glasgow more than anywhere else in Scotland."
Ms Levin has just published a report on her findings. She explained that although the 15 to 16 year-olds who were interviewed for her survey may not have been directly hit by job losses or changes to the welfare system, they still may have been affected by them: "If there is job insecurity or that type of pressure in the home, it is bound to put a lot of pressure on families.
"If someone loses their job, or their job has been threatened, this would put a tremendous pressure on relationships and put a stress over the household."
The report, No Mean City, examines why Glaswegian adults have the worst health in Scotland while the health of young people is similar to those in the rest of the country, by comparing the behaviours of adolescents in Glasgow with those in the rest of Scotland. This stage of life is seen as pivotal in determining the long-term behaviour of an individual.
Ms Levin explained: "Adolescence is a very important time as it is when people become independent and start to make their own choices. If a bad choice is made as a young person, such as smoking, then they are more likely to be a smoker into adulthood. Making other choices, such as sitting exams or who your peer group is, all have a great influence into adulthood."
Surprisingly, although smoking and drinking are major elements in the poor health of the city's adult population, the research discovered these habits were less prevalent in young people in Glasgow than elsewhere in the country. But aggressive behaviour, poor diet and sedentary behaviour were more common in this city than the rest of Scotland.
Ms Levin suggests more focus could be placed on reducing the inactivity of young Glaswegians, which tends to be overlooked as a factor in unhappiness in favour of initiatives promoting physical activity or improving diet.
"One of the key targets should be to reduce sedentary behaviour as well as increasing physical activity to combat obesity, although it is particularly difficult. You could play basketball for an hour, then sit on your computer for four hours, and that won't be overcome by the physical activity."
She notes the causes of sedentary behaviour, watching television, playing a games console or sitting on the computer generally occur in the home and suggests parents could be more aware of this but understands the difficulty of breaking habits: "If parents ask other parents how long their children play computer games and they discover the whole community is spending hours on games, then it becomes the norm.
"However it is important to get the message across that sedentary behaviour is not a good thing."
Co-author David Walsh, from the Glasgow Centre of Population Health, believes research into the health of adolescents could help unlock why life expectancy in Scotland is the lowest in Western Europe, the difference most markedly pronounced amongst those of working ages. He said: "This is important research into the life course; how health changes from childhood through to adolescence and then adulthood.
"It is important young people get the message of good health behaviours but it should be done in tandem with creating an environment that allows that to happen.."