The three winners were selected for their "creativity and their potential to engage with and serve the local community" as part of a competition launched by the Department for Transport last year.
The reviled Pacers, which were brought into service in the 1980s and comprise a modified bus body on a freight-wagon-inspired underframe, were supposed to have been phased out last year but will still be running this summer.
And describing the competition, Transport Secretary Grant Shapps said: “As their three decades of service comes to an overdue end, it is satisfying to know that new life for three of the last Pacer trains will ensure future generations can experience them in a different light.”
Platform 1, a men’s mental health charity, will be converting their Pacer into a kitchen to teach cooking skills to those they support.
The charity, located at the former Platform 1 of Huddersfield Station, already use retired train carriages as a safe space, counselling and learning environment to help hundreds of local men deal with mental health issues.
Airedale NHS Trust plan to transform their carriage into a mixed-use, non-clinical space to improve the experience of patients using Airedale General Hospital in West Yorkshire.
With a particular focus on helping children and families, as well as those suffering with dementia, it will provide a communal environment to support patients during their stay.
Fagley Primary School, based in Bradford, will set the Pacer up as a new science lab for students, helping promote learning in science, technology, engineering and mathematics. The train carriage will also benefit the wider community, who will have access to the space for talks and events.
The winners were announced on last night's 'The One Show' on BBC One and Platform 1 was profiled as part of the show alongside other shortlisted entrants. The programme spoke to staff, volunteers and people whose lives have been improved by the mental health charity.
Head Judge Pete Waterman, a record producer and keen railway enthusiast said: “The railway has always been very good at recycling its old assets.
"Lots of communities have benefited from this action over the years , we only have to look at the preserved railways and what they mean to rural communities.
"Where passengers might not miss the Pacers – their loss to the railways are these organisations' gain.”
The Department for Transport will now work with the winners to start on the installation and conversion of the former train carriages.
It emerged last year a Pacer train will become a museum piece following the Northern fleet's retirement from service this winter.
Leasing company Angel Trains confirmed they have donated a Pacer to the National Railway Museum in York, where it will go on public display.