Numerous dead were sleeping when their houses collapsed after being struck by intense bursts of lightning.
Forty-three people died there as the wind speed touched 130kms/h, said Relief Commissioner Sanjay Kumar of Uttar Pradesh state.
The MET department issued the warning even as the two north Indian states were reeling under the impact of a severe overnight dust storm that killed almost 100 people and left a trail of destruction.
TRT World's Arabella Munro has more on the story.
Alwar hotel owner Shivam Lohia said he abandoned his auto after it was nearly blown off the road.
"There was the clanking sound of tin roofs being blown away and motorcycles getting dragged", he said. "It was a nightmare", Lohia said. Another 35 are confirmed to have died in Rajasthan and two each in Uttarakhand and Madhya Pradesh.
Another 14 people were killed in Andhra Pradesh, which was hit by more than 41,000 lightning strikes late Tuesday.
Congress president Rahul Gandhi today urged his party workers to offer all help to the families of those affected by the dust storm in Rajasthan and Uttar Pradesh.
Some of the most severe damage was reported in Agra, the northern Indian city that's home to the Taj Mahal.
But the toll has tragically passed the 100-mark, with the northern states of Uttar Pradesh, Rajasthan and Punjab worst affected.
Most of the deaths were caused by house collapses and uprooted trees. Reports said the wall of an educational institution collapsed, killing 23 persons and injuring 21.
Rescuers were still going through the rubble of felled homes on Thursday.
In Rajasthan, while the official figures were of 33 deaths, unofficial sources pegged the casualties at 39.
46 in Agra district alone.
Rajasthan's disaster management secretary Hemant Kumar Gera said some were undergoing primary treatment.
TRT World spoke to Rebecca Bundhun from Mumbai.
A combination of violent wind gusts, dust clouds and smashing thunderstorms are devastating India, and it is only the beginning according to meteorologists. The damage done by dust storm in Bharatpur was huge as 138 persons suffered injuries, while in Dholpur 50 persons and in Alwar 17 persons received injuries, says, the state government's official figures.
A woman walks with her face covered during a dust storm in New Delhi on Wednesday.
Charan Singh, a scientist at India Meteorological department, said winds of 132 km per hour hit Agra, while even in the capital Delhi there were gusts of 59 km per hour. "It will take us at least two days to restore supply", said an engineer with the Alwar power company.
Family members of those dead will get Rs 4 lakhs as compensation, and those injured will get between Rs 60,000 and Rs 2 lakhs.
Dozens of people are killed and more than 100 others are injured after a powerful rain storms hit northern and western regions in India.