At the main train station
Praha hlavní nádraží (Prague Main Station) has coin- or card-operated luggage lockers in a range of sizes, plus a staffed left-luggage counter for oversized bags. It's the obvious choice if you're arriving by train with hours to kill before check-in, or leaving by train later the same day.
At the airport
Václav Havel Airport has a left-luggage service where staff store your bags for a fee per item per day — useful for an early arrival with a late check-in, or a long layover-style stopover.
Independent storage in the centre
A number of independent left-luggage shops operate around the Old Town and near the main squares, generally cheaper than hotel storage if you're not a guest, and handy if your accommodation won't hold bags outside check-in hours. Look for one with clear per-hour or per-day pricing and a proper claim ticket system — as with anywhere handling your bags, a visible, reviewed storefront beats an unmarked door.
A simpler option
Many hotels, hostels and short-term rentals in Prague will hold luggage for free on your check-out day even if your room isn't ready yet, or before check-in on your arrival day — it's always worth asking your accommodation first, before paying for storage elsewhere.