In Japan, there are some rural area (like my hometown), there are many places you can not use IC prepaid transportation cards. But generally if you visit Japan first time, it can be bigger cities like Tokyo, Osaka & Kyoto, Fukuoka, Nagoya, Sapporo…
Each cities and companies have something unique IC cards but generally you can travel Japanese metro cities with Suica (JR East), or ICOCA (JR West). It is true that you have to pay the deposit of ¥500, but it is QUITE convenient to use, and even some companies (especially in Tokyo), they discount few percents for IC card users.
They are my IC cards.
From top to the bottom, Suica (special design for mono-rail, bought in Haneda Airport mono-rail Station,) Suica (oldest one, guess using more than 15 years), and Icoca.
Recently I rarely use them, I use Mobile Suica in my iPhone 8 Plus.
Guess change your iPhone’s region to Japan, guess you fill find you can add Suica. Scan your Suica to take into your iPhone Wallet. Attention, that mono-rail one is not allowed to scan. Once you get your Suica card on your iPhone, you can not use your exact card again, the deposit (¥500) is moved to the balance.
Or submit Suica App and get Suica on your iPhone directly, I used my Japanese credit card, but whether it is available for your credit cards what was issued in out of Japan.
(I guess there are only describing in Japanese only, at least I could not find my Suica App in English or Chinese.)
You can buy these IC cards in JR stations, but when you are in Osaka, you can not buy Suica, and when you are in Fukuoka, you can buy neither Suica or Icoca, they have another IC card.
I recharge to my Suica by my bank card (through my Mobile-Suica App).
You can recharge your exact IC cards on the convenience stores (7-11, Lawson, Familymart), and stations. Guess you can not recharge on the buses.
Of course you can pay in those IC cards in convenience stores and many stores, generally chain stores, or even in automatic venders (especially Tokyo area).
It was surprising and shocking that I could rarely find I can pay at small stores in the stations or automatic venders in Kyoto/ Osaka/ Nara area in 2018. I rarely use coins in Tokyo.
In Kkday, I found there are two services, one is Suica in Tokyo, and another is ICOCA in Osaka. To be honest, I think they are a little bit expensive. But it can be convenient you have no need to keep the long line in front of the counters at the stations in the airport.
Both ICOCA and Suica are valid for 10 years. If card is not activated for 10 consecutive years, it may be invalid.