Five-month-old Tyler Rees has two types of "flat head" syndrome which has left both the side and back of his head misshapen.
His mother Chantelle, 22, wants to buy a 2,000 helmet which could protect his unusually soft skull and stop it becoming more misshapen.
Tyler's is a rare case because he has both the brachycephaly and plagiocephaly forms of the condition.
Mrs Rees, of Colinton, who is on maternity leave from her job as a carer, said: "It's been very noticeable and I have to do something.
"The only option for him just now is to be fitted with this special helmet but, for some reason, you can't get that done on the NHS.
"We're not a high-income family and can't just pull 2,000 out to do this, so we decided to launch an appeal instead.
"Tyler is a really happy baby just now because he doesn't know, but I don't want him to grow up with this having harmed him."
Mrs Rees's husband Stefan, 23, is a lance corporal with the 3 Rifles currently serving in Afghanistan.
"The last time he saw Tyler he was only 15 days old," she said. "A lot has happened since then. He can smile and make expressions.
"It isn't easy for Stefan knowing Tyler's going through this.
"Thankfully there are other mums around, including one whose daughter had flat head syndrome, and I can get help and advice from them."
Tyler could be fitted with the protective helmet at a private clinic in Bothwell and Mrs Rees hopes to raise the money needed within eight weeks.
"I only launched it the other day and got 200 straight away from friends and family," she said.
"Now I've made a couple of websites and just hope people's generosity sees us through."
While help from the NHS is available to babies with the condition – which can lead to the brain being pushed to the front part of the head, causing potential mobility problems – the fitting and purchase of the specialist helmets is not part of it.
That ruling has been the subject of charity campaigns across the UK, but no decision has yet been taking to change the policy. The UK-wide NHS said helmets were not funded nationally because there was insufficient evidence of clinical benefit of using the helmets. It is still regarded by experts a cosmetic issue.
Mrs Rees added: "I do feel like it's unfair. We both pay our taxes for the NHS and it could make a big difference to his life.
"If we manage to raise above 2000, the rest will go straight to a charity supporting others in our position."
To donate, visit www.justgiving.com/Jane-Louise0.