The ruling came on 5 November in a case involving 10-year-old twins adopted by a Czech-French couple.
The Czech man and his French husband adopted the boys as new-born babies in San Francisco, where they live.
However, the children spend their holidays with their grandmother in the Czech Republic, where their fathers previously had no rights over them.
Their Czech father told the Mladá fronta Dnes newspaper that the ruling meant his children would be granted Czech citizenship, which would make traveling to Europe a lot easier.
The landmark decision was allowed by a change in the law, whereby Czech courts may recognize foreign rulings on adoption, and sets a precedent for other gay couples.
Gay couples in the Czech Republic have been pushing for the right to adopt the biological children of their partners for years.
An amendment to the registered partnership law which would allow this has been in parliament for over a year, but has not been put on the agenda.
According to a June opinion poll, 49% of Czechs oppose joint adoption by gay couples (compared to 44% who support it), though 59% support step-child adoption.