An attacking midfielder, Kira has scored five goals in 12 internationals for the Nadeshiko.
The 2014 Asian Cup winner joins City after a 10-year career at Japanese top flight club Urawa Reds.
"Australia was the first country I ever visited, and I still would consider it to be my favourite country -- I've always wanted to come over here to play," Kira said.
"Melbourne City has been a great story over the last few seasons and are a successful club that I really wanted to be a part of.
"This will be my first time playing outside of Japan and I can't wait to get started at City and meet all of my teammates."
Kira, who is completing her hotel quarantine period, will add much-needed experience and goal-scoring power.
"To have someone of Kira's class and experience join our program during these challenging times is testament to the reputation our women's league program has built up around the world," City football director Michael Petrillo said.
"Kira is a technically-gifted attacking midfielder with a penchant for goals and will add creativity and a goal-scoring threat to our midfield and front third.
"I think she will be a player who will add real class to the W-League competition."
Checker, who has five national team caps, left the W-League to join French club FC Fleury 91 but had her time in Europe cut short by a stress fracture in her fibula.
The 24-year-old previously played every game in City's 2019-20 premiership-championship double and is set to pair fellow Matilda Jenna McCormick in defence.
City were due to open their campaign against Sydney FC on Dec. 30 but that game is now likely to be postponed due to Victoria's border closure.