The social justice agency Extern, which offers help and advocacy to 20,000 people across 27 counties, has warned that Brexit will have a disastrous impact on the future of those people - as it will affect their funding.
Extern also said it will affect their ability to move people freely to their haven centres in Northern Ireland.
The organisation which employs 600 staff supports people living with homelessness, children at risk of entry into care or the justice system, young people skipping school, mental health issues, those with problematic drug and alcohol use, and refugee resettlement.
Speaking at the launch of their new strategy for 2019-2022 at Thomond Park in Limerick, Extern's Chief Executive Charlie Mack said there were real risks to vulnerable young people and families as a result of Brexit.
He said the Budget 2020 provided €1.2 billion to business and tourism to cope with Brexit, but unbelievably there was no contingency for charities.
He said the UK Government had yet to publish detailed information on replacement funding to the community and voluntary sector working with these groups.
Brexit is also likely to have a significant impact on currency fluctuations which could also affect Extern and being able to easily access their 'safe haven' service in both counties Fermanagh and Down, particularly for young people could also be made more difficult by Brexit.
Mr Mack said 2,400 children from across Ireland need to stay at their Roscor youth village facility beside Lough Erne for respite, and when they need to leave their homes in times of crisis. "Where will they go if there is a hard border," he asked.
Extern gets referrals for its work from both Tusla and the HSE.
It operates the Janus Justice project in Limerick which works intensely with troubled young people who have been through the justice system.
It also runs youth outreach programmes and cross border youth training programmes.
97% of the young people it helped last year, many deemed difficult to reach, said they felt Extern helped them take better care of themselves, and 88% were enabled to stay in, or return to school.
The organisation hopes to secure an additional €10m in funding to enable an additional 5,000 people to avail of their services by the end of their news strategy period