The government wants a new body to oversee all of Scotland's enterprise and skills agencies.
On Wednesday, MSPs voted for a motion demanding that HIE retain its own board.
During First Minister's Questions at Holyrood, Ms Sturgeon said the vote would be "fully taken into account".
She said HIE's headquarters and chief executive would remain in Inverness.
The government is in a second phase of determining the future shape of enterprise and skills services provision in Scotland.
Liberal Democrat MSP Tavish Scott had asked the first minister to confirm the board of HIE would be kept after Wednesday's vote.
The Scottish government will reflect carefully on calls to allow Highlands and Islands Enterprise its own board, Nicola Sturgeon has said.