There are three official counts of Bohemian uprising culminating in the defenestration of officials:
1) In 1419 a Hussite crowd killed town council members in the then New Town of Prague. Notably, Hussites were a movement of reformed Christians a hundred years before Protestantism. This first official defenestration triggered the Bohemian Wars a struggle for power between Catholics and Hussites.
2) In 1483 a violent mob ejected the mayor of the Old Town of Prague through a window of the town hall. It established equal rights between the Hussites and Roman Catholics.
3) In 1618 the Catholic counts Martinice and Slavata were thrown out of a window in the K̵a̵r̵l̵š̵t̵e̵j̵n̵ Castle of Prague after they ordered to halt the construction of a Protestant church. Eventually it sparked the Thirty Years‘ War.
Most notably there is also:
4) the suicide declared murder of the foreign minister of Czechoslovakia Jan Masaryk in 1948 by Russian agents is also referred to by the „4th defenestration of Prague“. Although used with an ironic undertone AFAIK.