Medicine in Japan
It can be aggravating for many, but laws regarding medication in Japan are extremely strict, and if you want to make sure you have a trouble-free (and healthy!) experience you need to do your due diligence. The last thing you need during your trip is to take a half-day going to a doctor, or problems at customs that can ruin a trip.
Bringing in Medicine
We can't give any legal advice for this, but the general rule is that if your medication includes stimulants (such as pseudo-ephedrine or Adderrall) or opiates (like codeine) they are illegal in Japan. If you are unsure, please check ahead of time, as many over-the-counter cold or allergy medications fall into the banned categories.
Up to a two-month supply of non-prescription and one-month of prescription medication can be brought to Japan. If you need more, you will need to get special permission in advance (link below).
Even the most basic medicines such as aspirin or ibuprofen need to be purchased from a store that has a licensed person on staff. Convenience stores and supermarkets do not tend to fall into this category, so look for a shop that has 薬 (kusuri) on a sign, and be sure to go during daytime hours. Even 24 hour stores do not usually have a licensed person on staff during the night. When you do go, it's going to be helpful to have the name of what you want written out, ideally in Japanese, and be sure to ask the staff about dosage since the packaging is all in Japanese.
Filling a prescription
Japanese pharmacies won't fill a foreign prescription (and many medicines are unavailable anyway) so if you have an emergency you need to go and see a doctor. If you're at a hotel it's best to ask the staff for a doctor that can communicate with you, but if you're in a rural area that may be difficult so please be aware. Otherwise, your best bet in the city is to find a hospital that specializes in foreign patients, though it will cost a bit more.
Once you have your prescription you'll need to go to a nearby pharmacy. Often a "drug store" is only for over-the-counter medications, so you'll need to go to an actual pharmacy, and these often have limited hours. The clinic that writes the prescription will be able to show you where to go to get it filled.