The first (and arguably most important) step to preparing for studying abroad is acquiring a student visa. It's a simple process that takes 4-5 business days, but get it done ASAP to leave time for potential mishaps. You can also choose to depart for Japan before the semester starts (spring semester starts in April)!
Certificate of Eligibility
Normal Visas are good for 90 days. Because you will be entering Japan as a student, you need to apply for a student visa which is generally good for 1 to 5 years. The first step in obtaining one is to apply for a certificate of eligibility from your host university (they will send you an email with information on how to apply). You CANNOT apply for a visa without this.
The Japanese school calendar is different from the American so plan to wait a little while to receive your certificate. I applied in the beginning of January and received it one month later.
Apply at the Japanese Consulate
After you have received your certificate of eligibility, head down to the Japanese Consulate General in Nu'uanu with your:
Valid Passport (properly signed by bearer, w/ at least 2 blank visa pages)
One passport-sized photo (2”×2”, taken within six months)
*Attached to the application form using GLUE ONLY, do not staple or tape.
Certificate of Eligibility (original)
Registered alien card (Green Card) or US visa with I-20 and I-94 for non-US citizen
Give all the documents to the attendant and you will be in and out of there in a few minutes. Make sure to fill out the application before arriving. It makes things easier for you and the staff.
Your Visa will be ready in 4 - 5 business days. All you need to do is go back to the consulate and pick it up! Don't forget to bring the receipt! You will need to sign and return it to the staff.