Sports in Japan are certainly co-ed. Most junior high and high school students will either join a club or play school sports of some kind. In elementary school, kids will usually do several extracurricular activities, like learning a musical instrument, taking ballet lessons, or playing soccer. Add to that a decent PE curriculum including very important Sports Day competitions, and it's difficult to find someone who didn't at least try a sport of some kind during their childhood.
That said, men's sports are still basically men's sports. The major league sports are men-only: baseball, sumo wrestling (okay, not a league, but still...), soccer, basketball. Women play these sports, but there's rarely a true full professional league - the national teams are popular and especially talked about during international competitions, but there aren't many places to see women's sports competitions in Japan.
So, I just contradicted myself there - baseball still is essentially a man's sport. I haven't heard of any girls playing in the Koshien high school tournament. In fact, as of the 2016 season, girls weren't permitted to be on the field and I don't know if that's changed. There are a few women who have made names playing in the semi-pro leagues (Ayumi Kataoka, manager of the Ibaraki Golden Golds, is the most well-known these days, along with Eri Yoshida, a knuckleball pitcher).
And there's the JWBL. I've posted about it before, so I won't go into too much detail, but when it comes to stars in that league, there is no name bigger than local lady Yuki Kawabata.
I say local because Saitama is the closest team to where I live now, and very close to where I used to live. In fact, their games were played not too far from my former apartment.
Anyway, she's probably the best player in the four-team league, and I'd argue the most popular as well. She had a .406 batting average in 2011, and in 2013 bested that with a .431 average. While her 2016 statistics showed an "off" year of .327, this season she hit .397, bringing her career average up to .377. That's pretty impressive, I'd say.
I still haven't decided if I want to torture myself by trying to get a full set of the JWBL Epoch autographs from 2016 - that's 79 cards (or 78 if you ignore the celebrity autograph). Epoch didn't issue a set in 2017, so that may have been just a one-off set. But I hope it comes back in 2018!