Apple kept all the 10 retail stores in the country closed for months due to health risks rising out of the coronavirus pandemic.
The iPhone maker's stores located in Fukuoka and Nagoya Sakae will reopen on Wednesday.
The company is yet to reveal the reopening dates for other eight retail stores in the country.
"Our commitment is to only move forward with a reopening once we're confident we can safely return to serving customers from our stores," Apple said in a statement last week.
"We look at every available piece of data -- including local cases, near and long-term trends, and guidance from national and local health officials. These are not decisions we rush into -- and a store opening in no way means that we won't take the preventative step of closing it again should local conditions warrant," it added.
Japanese Prime Minister Shinzo Abe on Monday lifted the country's nationwide state of emergency, ending restrictions in the remaining areas where the order was still in effect due to the COVID-19 pandemic.
He said the country had managed to control the spread of COVID-19 since issuing the order in some areas on April 7, then later extending it nationwide, according to a report in BBC.
While Apple closed nearly all of its retail stores worldwide in response to Covid-19, nearly 100 of its stores globally have now reopened.