Henry, 30, missed Ireland's game against South Africa on 8 November because of an unspecified illness.
Following further tests, the Irish Rugby Football Union revealed the extent of Henry's condition on Monday.
"Tests have shown he suffered a temporary blockage of a small blood vessel in his brain," said the IRFU.
Henry is facing a lengthy lay-off following the diagnosis, although Ulster and Ireland officials are confident he will be able to resume his rugby career in a matter of months.
"He is at home now and is well but needs further investigation and specialist opinion," added the IRFU statement.
Medical opinion last week was that Henry was suffering from a severe migraine but a more serious diagnosis has now been arrived at.
The back-rower started in all of Ireland's Six Nations matches this year as they clinched the title and brought his caps haul up to 16 by playing in both summer Tests against Argentina.
With Sean O'Brien currently out of action, Henry looked to have a strong chance of holding onto his Ireland starting role next spring.
The flanker's lengthy absence will be an even bigger blow for Ulster as they attempt to regroup after their poor start to the European campaign.
Henry earned his first Ireland cap against Australia in June 2010, by which time he was already regularly captaining Ulster and had just been named as the province's player of the year.
He helped Ulster reach the 2012 Heineken Cup final but while he was a regular member of the Ireland squad, he was unable to hold down a regular place because of the form of O'Brien and Peter O'Mahony.
He missed the final three matches of the 2013 Six Nations because of a knee injury after coming on as a replacement in the opening two games against Wales and England but started in all five games in 2014, helping set up crucial try in the championship-clinching victory over France in Paris.
Ulster and Ireland flanker Chris Henry will be out of rugby for some time after tests revealed that he has a blocked blood vessel in his brain.