From u/mushiiiiii

Having somewhat recently run into a panic of how one acquires the morning after pill in Japan i thought I’d share some more updated info for all of you ladies and gents.
I reside in the Tokyo area, so my insight is applies to this general region. Prices may vary depending on region.

Names for “The Morning After Pill”

In Japanese it’s called 緊急避妊法 (Kinkyū hinin-hō).
However, it may also be referred to as listed below.
モーニングアフターピル (mo-ningu afutaa piru, morning after pill)
アフターピル (afutaa piru, after pill)

Other Info

The Morning After Pill is not sold over-the-counter so a prescription from a doctor will be required.
It is not covered by insurance.
I personally would say DO NOT order The Morning After Pills online or have it shipped to you from overseas. I’ve heard the horror stories about shipping other kinds of medicine /pills from overseas and I personally would not recommend it.
There are two types (that i know of):
I was told the effectiveness of both pills are the same.
Please keep in mind that prices may vary depending on location and clinic.
1) A single pill you take once. The cost is can range from about 17,500 JPY ~25,000JPY (prices i received from calling around Tokyo October 2016) .
2) Two pills. You take one and take the second pill 12 hours after having taken the first pill. This option can lead to nausea and vomiting, so often times you are provided with additional pills to help combat this. For me the whole package (the 2 actual morning after pills and the 4~6 anti-nausea/vomiting pills) cost about 7,200JPY (October 2016). However, I have heard that in Oita i can be found for 5,400JPY (2015) and in Shibuya for as low as about 2,800JPY.

Clinics that I and others below have recommended…

Tokyo Area

Ikebukuro:
Ikebukuro Clinic・池袋クリニック : Though it cost a bit more, i was guaranteed an appointment and prescription and they took time to explain things in full and answer all my questions. They also had the required forms in an English version which helped settle my already very flustered self.
Shinjuku:
K Ladies Clinic・Kレディースクリニック : I’ve read/hear great things about them and that they’re quite English friendly. Though I don’t know which one it was, it seems a Morning After Pill can be acquired for about 10,000JPY here according to a comment below.
Shibuya:
Jasmine Lady’s Clinic ・ジャスミンレディースクリニック : A life saver that has kindly been mentioned in the below comments. Though I don’t know which one it was, a morning after pill may be acquired for the more affordable price of about 2,800 JPY if you are a student, it is slighty more expensive without the student discount.

*Featured image from Google. Used without permission.