Unison argued that the structure of the fees discriminates against women and ethnic minorities. Currently for an employee to start an action and bring it to tribunal can cost upwards of £1,000.
In his ruling, the Hon. Mr Justice Foskett admitted that although it is likely there have been instances where individuals have been refused access to justice as a result of the fees, the "assessment has to be seen as speculative until convincing evidence to that effect is uncovered".
It is the second time Unison has failed in a legal challenge against the validity of the fees, after a court ruled its first attempt was "premature" in February of this year.
The union has vowed to appeal the decision, with general secretary Dave Prentis calling the High Court ruling a "missed opportunity" to restore access to justice for employees.
Eversheds partner Geoffrey Mead said that despite the ruling, many employment groups still believe fees are too high.
"Furthermore, a change in government at the election next year could result in a significant reduction in fee levels: both the Labour party and Liberal Democrats have indicated that they would reduce fees," he said.
While Nicola Ihnatowicz, employment partner at law firm Trowers & Hamlins, said employers will be "relieved" that the number of cases is not likely to increase in the short term.
"Certainly we're seeing that the claims being brought are those that are higher value and more complex, including those involving multiple claimants; these are the claims that justify a risk on the fee," she added.
"Lower-value claims for individuals, such as claims for redundancy pay or maternity rights, are now far less common."