It can be done, but it's not automatic.

Formaly you need get children into school and headmaster can allow homeschooling. After that school need to check what children learned (i think 1 times per year)

There are homeschooling friendly schools (for example “ježek bez klece” translated as “Hedgehog without a cage” which are without problem, Ježek bez klece itself operate on Self-Directed Education and they know specifics of homeschoolings. But if you choose some without understanding, you can have problem.