Ms Hyslop is to undertake "an intensive week of activity" focusing on business, trade, tourism, education and culture.
She will meet business leaders in Tokyo and Nagasaki to promote Scotland as a place to invest and do business.
The cabinet secretary said Japan was "a very important international partner for Scotland".
The Scottish government said Japan was one of the top 20 destinations for Scottish exports, and was the seventh largest source of foreign direct investment with Japanese firms employing 6,250 people in Scotland.
Ms Hyslop, who previously visited Japan in 2015, will meet senior figures from companies which are already investing in Scotland, such as Mitsubishi, life sciences firm Kyowa Hakko Kirin and medical firm Reprocell.
She said: "Scotland and Japan have much in common - a wealth of expertise, a passion for innovation, a highly educated and skilled workforce, and a desire for increased international collaboration across all sectors.
"There will be much to share and much to discuss during my time there, including providing reassurance that, despite the UK's vote to leave the EU, Scotland remains a progressive, outward-looking internationalist country that is open for business and ripe for investment.
"I'm confident our dialogue will deliver mutual benefits."
Scottish External Affairs Secretary Fiona Hyslop is to travel to Japan to promote the message that Scotland is "open for business".