The poorest pupils could miss out on the vocationally-led 14-19 learning pathways because they cannot afford to buy resources for vocational courses, according to Barnardo's Cymru.
The youth charity claims many youngsters studying subjects such as sport and art are too embarrassed to ask for financial support even when it is available to them.
Barnardo's is calling for "non-stigmatising" financial support for the most deprived families and clear guidance for young people on what grants are available.
Dr Sam Clutton from the charity's policy unit said no money has been ringfenced for the cost of vocational and practical courses, which will be promoted alongside traditional A-levels as part of the learning pathways.
"Young people from the most disadvantaged backgrounds will not have genuine choice if they cannot afford the additional costs and we are convinced this will impact on participation rates," he said.
"Even when young people have the option of applying for help with equipment costs, evidence from mainstream education suggests that young people are not aware of it or are too embarrassed to seek help."
But Gareth Jones, secretary of school leaders' union ASCL Cymru, said schools rather than individual pupils would be hit by the high costs of vocational courses.
"As I understand it, any resources that are required for activities that are compulsory are paid for by the school - certainly up to the age of 16. But as regards institutions, there's no doubt that the 14-19 curriculum is going to be more expensive."
An Assembly government spokesperson said local authorities will receive about pound;30 million to fund the learning pathways.
"They are able to use the funding towards the cost of developing vocational courses, including for the purchase of equipment for use by students on these courses (for example the purchase of hand tools) but there is no provision for any direct payments to be made to students."
The spokesperson said poorer students could access education maintenance allowances and could apply for hardship grants from their colleges.
Philip Dixon, director of education union ATL Cymru, said schools and colleges had learnt to approach financial issues carefully.
"Teachers have been very sensitive about the way that they support pupils who do not come from well-off families. For example, in the case of free school meals only the young person themselves knows if they are getting a free meal or not.
"I believe any school or college principal would make sure that youngsters were not put off doing a particular course just because they are from a disadvantaged background. They possibly need to do more to reassure young people about this."
But Dr Dixon admitted there are problems surrounding the funding of school trips.
"These are more voluntary and pleasurable and some young people do miss out on them."
Barnardo's Cymru has also called on the Assembly government to issue advice and support to Communities First Partnerships on the role they could play in providing volunteering opportunities.
Dr Clutton said: "The reality is that these activities often have hidden costs and the most vulnerable young people who could benefit hugely by taking part in these schemes might be excluded because they can't afford it."
The Assembly government said projects such as young Millennium Volunteers Wales and GwirVol were geared up to providing training and volunteering opportunities for young people.