I've seen quite a few fanfics where the series takes place in a high school. Personally I don't have much problem with this type of fic provided it makes sense, i.e Ranma, Sailormoon, Azumanga Daioh; not Slayers or Bubble Gum Crisis. Even when it does make sense for the series it often annoys me because the fic is supposedly set in Japan not the USA and the high school described in the fics generally do not resemble Japanese high schools.
Some points I want to make:
Japanese upper secondary school kōtōgakkō is roughly equivalent to 10-12 grade in the US. Ninth grade would still be part of Junior High school (chūgakkō -which is 7-9 grade).
Japanese high school is not mandatory so no truancy officer would stop the kid and bring them to school.
High school in Japan is not free parents have to pay to send their kids there so parents generally care if their kids are doing well, unlike in the USA where some parents just don't care and only send their kids there because the law says they have to.
School hours are from 7:45am to 3:50pm (of course this does vary some between schools but that is a common time frame and there are after school activities). School is generally around 8 hours.
Most schools have school uniforms. A summer and a winter Uniform. You do not get to decide whether to wear the summer uniform or winter one just by if you are cold or not. There is a day called "koromo-gae" (changing of the clothes) where everyone in Japan changes from winter to summer uniform or vice versa. Most schools do not allow accessories and if they do it generally has to be a solid color.
When students get to school the first thing they generally do is take off their outdoor shoes and put on indoor slippers. This is followed by going to their lockers and putting in or taking out books for class.
Students then go to their homerooms in which they will spend most of the school day in, unlike the USA where the children walk from classroom to classroom. In Japan the students stay in one class room all day (baring a class requiring another room like gym or home economics) and the teachers change classrooms. When a teacher enters the room the students are supposed to stand up and then bow to the teacher, they are also expected to bow at the end of class when the teacher leaves. Between classes there is a roughly 10 minute time period which, if the student doesn't have to go to the bathroom or switch classes, is basically free time. The students can play cards, read manga, fix their hair, talk to their friends, wander to another class and talk to a friend in that class, etc.
Lunch is usually brought from home in boxes called Bentos. Bento's usually have rice and a couple side dishes. Appearance is important people because people will comment on how nice it looks or how bad it looks. Schools generally sell some foods like bread on school grounds if you want to buy a lunch, they also are likely to have vending machines which the students can buy a variety of things like tea or coffee. Lunch is usually eaten in the classroom but most schools allow you to eat them outside on school grounds if you want. Lunch time varies by school but is generally around 45 minutes long. Some schools do not offer lunches, in those schools all meals have to be brought from home.
At the end of the day 15 minutes or so is spent on cleaning up the school. It is the students job to clean the classrooms. During the begining of the year the class is divided into groups and whatever groups turn to clean does it. Every few month's there is a big cleaning of the school where the students clean the toilets, library, bike parks, weed the lawns, hallways, clean the Head Master's office, etc.
Japanese schools do not have proms.
There are quite a few after school clubs and activities that students are encouraged to join. There are various sports clubs like Kendo, Volleyball, Swimming, etc., as well as non-sports clubs like drama, band, or manga.
After school and after school activities many students go to Juku (cram school) to prepare for exams, get tutoring for classes, or take another class not offered at school like piano lessons but not all students do this (this like high school is not free).
Girls and guys are separated for sex education in Japan. Girls are taught by a girl, guys by a guy. Gym class is also divided between guys and girls though the teacher can be either male or female. Easily seen in Ranma where Akane is playing Softball, Ranma wasn't. Home economics used to be a girls only class but is now required by everyone.
Generally you take from between ten to fourteen classes at one time, but not every day the classes rotate. Ex. Monday may have English, Tuesday at that time could be History.
Schools have regulations that can extend beyond the school time for example some school do not allow students to have after school jobs, have required haircuts, or have curfews for the students (in the case of curfews a couple teachers will go to places students hang out and send them home -can be seen in the movie Zebra Man).
School starts in April. Summer break is not until near the end of July so students are usually given assignments to do over the break (summer does not divide the school years it's during the school year). Summer is usually around a month long, not multiple months.
Once a year the schools do a cultural festival usually in the fall. It is a big festival put on by the school, where you sell tickets and let people off the street in. Money raised goes to the school funds. It lasts from a few days to a week. During this time the whole school is decorated, and each class and club puts on an event. The events are basically food shops, exhibitions, games, or sales. This can be seen in Azumanga Daioh.
Once (some schools have it twice) a year there is also a sports day where the school is divided into teams. Usually divided into 4 teams (more or less depends on number of students in the school). Various sporting events take place like running races or cheering competitions.
It is common to see students in the hallway or skipping class in Japan because most teachers do not take attendance or really care if you aren't in class. If you miss the stuff taught it's your problem.
During the final year of high school (also Junior High) students take a class trip to a famous place or occasionally a foreign country. These are meant to be a learning experience, either to view great places in Japanese history or expose the students to a different culture.
In older anime you will see kid punished by holding buckets of water in the hallway. This is rarely done anymore.