The storm began shortly before 7:00 pm (1900 GMT) in the town of Siguiri, close to the border with Mali, witness Mamadi Doumbouya, a local resident, told AFP.
He said eight children in total, accompanied by two of their mothers, were under a mango tree at the back of his house.
"I invited everyone to take shelter in my living room. The ladies rushed under my roof but the children stayed behind to make the last cups of tea," he added.
Lightning then struck the mango tree and when Doumbouya rushed out, all of the children were on the ground and unconscious, he said in a telephone call.
Six of the children -- five girls and a four-year-old boy -- died while being taken to hospital, he added.
A doctor from Siguiri Hospital said the six dead children were brought there in the early evening and two others were placed under observation for the coming days.
West Africa is currently undergoing its rainy season.
On Saturday a landslide hit a gold mine in the same area as Wednesday's storm, killing four people including a two-year-old girl and her mother.
"The victims were working in a former gold mine where mining was banned because of the risk of landslides" in the heavy rains, "but people were hiding to go to the tunnels", a Red Cross official said.
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