Which country are you living in at the moment? Methods of doing so might vary between countries, for example the UK and US.
I am not certain whether you want to spend your whole university education in Japan or not, so I'll assume this is about undergraduate study in Japan.
Before you read this, remember that I am in a similar situation (I want to study in China) and I am only speaking from my own experience. There may be far easier or more suitable ways, so I am not an expert on this matter.
If you're wanting to gain your full university education there (i.e. undergraduate degrees), then I suggest firstly researching and noting down universities/colleges you are thinking of studying at. Visit their websites, and I highly recommend you read through everything - application procedures, entry requirements; especially Japanese proficiency.
It's also best to contact the universities/colleges for advice before considering application - explain everything and what you want to study. You can send them a formal letter through the post, or most universities have email addresses for foreign affairs.
Seriously consider your reasons too. Don't just go there on a whim or because of an interest; choosing to do this is an enourmous and of course life-altering commitment if you go through with it, and you should have solid reasons why you want to go and why you don't want to study in your home country. You never really know - you might quickly become sick of studying there, or you might find it very stressful considering you will most likely take classes in Japanese. On the other hand, you might love it, and I hope you do.
As I said I am a student hoping to take my university education in China, so I guess my situation is a little similar. As for Japanese proficiency, I am quite sure most college/university lectures will be in Japanese, except for a select few at certain universities. It all depends on where and what you choose to study. Most university entry requirements will of course want Japanese proficiency, and I presume the university decides the level. My best assumption would be that before attending, you would certainly have to spend 2 years or more of language study to satisfy proficiency requirements.
Finances are very important. How will you be funding this education? Remember you will be funding not only the education, but living costs, travel costs, general spending (such as food), and any other fees including application fees. Universities or the Japanese government may offer scholarships which may pay for the education or more, and if you can gain them then you should certainly do so. Don't forget that you have to work hard for them though, especially to renew them.
Another important thing is to visit the univesities. It may seem very expensive to go all the way to Japan just to visit, but it's necessary and highly recommended. You are also likely to be asked for interviews too, which needless to say are very important to attend.
If you decide to study in Japan, you will need a student visa when you go. This would be gained at a far later stage though. Sponsorship from the educational institution/college/university you are attending is required, and you will also need to provide proof that you have the finances to support your study and stay in Japan.
Take note that on a student visa you may not engage in paid work unless you have permission from your university and immigration office. The hours you can work each week will be limited too. I think it would be very difficult to try and support yourself on a job alone, so think carefully about your finances.
All in all, this is not going to be easy at all, and you need to be fully committed to this. If you choose to do so, it will be expensive, complicated and of course - you will need to work hard. But don't let me put you off; if you have your heart and mind set on it then I'm sure it will be a very rewarding and learning experience for you. I wish you good luck.
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