The Court rejected Anheuser's claims that a bilateral trade agreement between the Czech Republic and Portugal had "infringed its right to the peaceful enjoyment of its possessions".
Anheuser said it had applied to register Budweiser as a trademark before the 1986 trade agreement came into force.
But the Court's judges ruled that America's biggest brewer was not in a strong enough legal position to mount a complaint. "The company could not be sure of being the holder of the trademark in question until after it had been definitively registered, and then only on condition that no objection was raised by a third party."
The ruling is a victory for Czech brewer Budejovicky Budvar in the latest tussle between it and Anheuser over the Budweiser brand name.
And, it is the first time the Court of Human Rights has dealt with a trademark dispute since it was set up in 1959 to deal with civil rights violations.
Now, its acceptance of the case has prompted questions over its future role in trademark cases.
Yet, a spokesperson for the Court told BeverageDaily.com that "this case was not a classic trademark dispute".
This is because it only concerned whether the simple request for a registered trademark was enough to give a firm property rights under the Court's law before that trademark had been fully registered.
"It is unlikely to inspire copycat claims since in any case the Court did not find a violation," said the Court spokesperson, adding that either party still has three months to ask for the case to go before a 17-member Grand Chamber.
The Court is currently handling around 80,000 cases, yet none are thought to be trademark disputes between firms.
The Anheuser- Budejovicky dispute has been running for decades, with court battles currently on-going in several countries around the world.
In Portugal, Budejovicky originally held the 'Budweiser Bier' trademark until this was retracted on Anheuser's request in 1995.
The Czech brewer challenged the decision using the 1986 treaty and won the rights back at the Supreme Court in 2001.
In another recent ruling on the issue, an Austrian Trial Court rejected Budejovicky's claim to sole rights on the 'Bud' name in the country, allowing Anheuser to sell its own Bud beer there.
The Court ruled that 'Bud' was not a place in the Czech Republic and so cannot be protected in Austria under a 1976 bilateral treaty signed by the two nations to protect products that have geographic indicators.