Michal Prasek's body was found in the pen of the nine-year-old big cat by his father, who said the enclosure was locked from the inside.
Mr Prasek, 34, kept the lion for breeding along with a lioness, which lived in a separate cage.
The cats were shot dead by police called to the scene in the village of Zdechov, in Vsetin District in the Zlin Region.
A police spokesperson told local media that the shootings were 'absolutely necessary for them to get to the man'.
Mr Prasek purchased the lion in 2016 and the lioness last year and kept the pair in enclosures he built himself in his back garden.
He was breeding them illegally and had been fined in the past because he did not have planning permission for the cages.