They were mistakenly painted on the Bregagh Road near Armoy by a contractor who had been doing work in the area.
The iconic tunnel of trees, known as the Dark Hedges, features as the Kingsroad in the smash-hit HBO television series.
Conservationists and fans had expressed their annoyance at the error.
The Department for Regional Development (DRD) said work began on Wednesday morning to remove the white lines and was completed by lunchtime.
It is the second setback for the Dark Hedges in just over a week.
At the end of January, Storm Gertrude ripped up two of the 200-year-old beeches that overhang the road and damaged a third.
Amateur photographer Bob McCallion, who lives in the area, welcomed the removal of the lines.
"I actually called the lines sacrilege because they just shouldn't be there and I'm glad to see them gone," he said.
"It's a step forward, but there's a lot of issues here.
"The road has actually been made wider recently which is not on.
"The verges need to be restored and the road brought back to its original width.
"It affects the overall visual impact of the place doing things like this and you've got to be very careful that you look at the whole area more or less like a conservation area and try to look after it."
White lines which were painted on a famous County Antrim road which featured in Game of Thrones have been removed.