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."

Striker Emmanuel, 27, scored 19 goals in the National League for Bromley last season and played for the Whites between 2012 and 2014.
Centre-back Howlett-Mundle, 19, has previously had spells at Crystal Palace and Scottish sides Hearts and Montrose.
Forward Jackson Jr, 19, had stints at Whitstable Town and Worthing last season and has agreed a two-year deal.
Meanwhile, 32-year-old former Welling player-manager Loui Fazakerley, who is a fitness coach at Crabble, has been registered as a player for the coming campaign.
Find all the latest football transfers on our dedicated page.

A selection of photos from Africa and of Africans elsewhere in the world this week:

Timothy Pawlett, 52, from Haverfordwest and Gareth Clement, 55, from Crymych, are alleged to have left Fishguard port early or arrived late while still claiming full working hours.
It meant they had been overpaid a combined total of over £1,800.
They both deny a single charge of fraud and the trial at Swansea Crown Court continues.
Prosecuting, Nicholas Gedge told the court Mr Pawlett was secretly logged leaving his post early or arriving late 72 times between 1 November 2015 and 17 February 2016.
Mr Clement was said to have left early on 54 occasions.
In some instances they had left two hours early.
It meant Mr Pawlett had been overpaid £1,100 and Mr Clement £710.
The alarm was raised when their boss, Det Sgt Ian Hardy could not find either of the officers before their shifts had ended.
"He was a little curious," said Mr Gedge, especially when he found both had recorded completing their full shifts.
The following night he parked outside Fishguard harbour and saw Mr Clement driving away 40 minutes early.
He drove to Mr Pawlett's home and saw his car already parked outside, which meant he must have left 30 minutes early.
Det Sgt Hardy asked for a camera with automatic vehicle number plate recognition technology to be checked and discovered "numerous" examples of them leaving early.
After their arrests neither officer disputed the data.
Mr Clement said he had been having personal and family difficulties while Mr Pawlett said he had been suffering from anxiety and depression.
Scottish External Affairs Secretary Fiona Hyslop is to travel to Japan to promote the message that Scotland is "open for business".
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Dover Athletic have re-signed Moses Emmanuel and brought in Jahmal Howlett-Mundle and Ira Jackson Jr.
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Images courtesy of AFP, AP, EPA, Getty Images and Reuters
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Two Pembrokeshire police officers left work early 126 times in three months, a jury has heard.