Stephen and Wendy Meek from Lanark have been campaigning since 2005 for a change in the law since the birth of their severely disabled son Justin, who cannot walk and is oxygen-dependent.
The couple argued in court that the Department of Work and Pensions regulations, which state that children under three are not entitled to the mobility component of Disability Living Allowance, contravened their son's human rights.
But this was rejected by Judge Lord Brodie at the Court of Session in Edinburgh.
In Justin's first year the Meeks had to spend £500 a month to use a disabled taxi service to make more than 150 visits to hospital.
Justin is now over five and eligible for mobility benefits, but the Meeks continued their fight on behalf of other families.
The charity Contact A Family said it was deeply disappointed at the ruling, because it affected around 7,000 of the most vulnerable disabled children in the UK.
Chief executive Srabani Sen said, 'Families with severely disabled young children are often left housebound because they don't get help towards travel costs. Some children need to travel with bulky life-saving equipment. It is not down to their age that they have mobility difficulties. And yet their families have to struggle without the mobility benefit for three years before it can be paid.'
She added, 'We applaud the Meek family's efforts to challenge this law on behalf of all other families with disabled children in the UK.'