There is a large number of pharmacies in České Budějovice (see the list here) and the most common opening hours are MO - FRI 7:30 - 17:00.
In case you need some kind of medicine in the evening, at night or over the weekend, when shops are normally closed, there is a non-stop pharmacy located conveniently in the Hospital of České Budějovice:
Emergency Pharmacy
Hospital of České Budějovice (Nemocnice České Budějovice) - entrance hall
B. Němcové 585/54
370 01 České Budějovice
Phone: 387 873 126; 387 873 103; 387 873 120
Opening hours: Mon– Sun: nonstop