The federation's arbitrary committee on Wednesday ruled in favour of Jan Sterba, a member of the Czech Republic's sprint kayak K4 crew, who tested positive for a banned stimulant during Olympic qualifying in Poland on May 17.
He was banned for six months by the federation this month, but appealed the decision.
Petr Mokry, a Czech canoe federation secretary, said officials are working on the necessary paperwork to make it possible for Sterba to compete at the Olympics.
Sterba acknowledged he used a food supplement called "Shot Gun" that contains the substance beta-methylphenylethylamine. He called the decision "great satisfaction."