Here are the steps from insurance to getting your medication.
Be Covered: Insurance
The first thing which is a must if you live here (at least officially) is that you have to have medical insurance. If you have a long-term visa, you should have organized health insurance from one of these companies. If you are a permanent resident, then you are entitled to participate in the public health insurance system. In either case, check that your doctor accepts the insurance company you have.
Book or Try your Luck
Broadly speaking, there are two ways to see your doctor. You can make an appointment, which may shorten the wait at the surgery but may mean you have to wait a week or more to see your doctor. Usually this is for more involved treatment.
If the matter is more urgent, or you are just feeling off color, then you can see the doctor during the office's operating hours (ordinační hodiny). The problem is several other people will be doing this, too. According to several experts - okay, family members - going in the afternoon increases your chances of a shorter wait time as those needing more attention tend to go in earlier. But there's no guarantee.
If you do want to try your luck, it is important to know who was the person who came before you so that you know your place in the queue. Once you know your place, be sure to guard it, because some people may try to jump in.
Free Health Cover, almost: the regulation fee
When visiting the doctor, there is a regulation fee of 30 CZK. This is either paid to the nurse/receptionist before seeing the doctor, or the office may have a ticketing machine. You place the required amount for the fee in it and it dispenses a ticket, which you then present to the nurse to show you've paid. Remember, the regulation fee only counts if you're covered by Czech public health insurance.
The fees are:
30 CZK for a doctor's visit (this includes specialists)
60 CZK per day of stay in hospital (if you visit a GP at a hospital you pay the above fee)
90 CZK for emergency treatment
Before seeing the doctor, you need to show proof of ID - e.g. your passport, and your means of insurance (either the card from your Czech Insurance company, or your EHIC if you're a European Union citizen).
Be Covered: Your Shoes
For GP visits you will be expected to put a protective covering on each shoe, called návlek. There is usually a container outside the doctor's door and a bin where to dispose of the used ones. Be sure not to confuse the two.
In some other circumstances you'll be expected to remove your shoes. The surgery will then provide slippers for you to wear.