At least two more people were killed in New Delhi.
In New Delhi, the police were seen clearing streets of debris and fallen trees.
Similar storms hit the region every year but this year has been the deadliest.
"Thunderstorm accompanied with gusty winds are also very likely at isolated places over Punjab, Haryana, Chandigarh, Delhi, west Uttar Pradesh, Vidharbha, Chhattisgarh, Bihar, Telangana, north coastal Andhra Pradesh, south interior Karnataka, Tamil Nadu, Puducherry, Lakshadweep and Kerala", the IMD had said in an advisory.
Forty people were killed by hail and thunderstorms that brought down walls, trees and power pylons in Uttar Pradesh state, T. P. Gupta of the state disaster management department told AFP.More news: Man City record will be tough to break-Guardiola
More news: Israel boosts Gaza border force as U.S. prepares to open Jerusalem embassy
More news: World Health Organization to send Ebola vaccines to DRC as virus spreads
Reports pouring in from Uttar Pradesh said almost 100 houses were gutted in a fire which broke out due to lightning in Sambhal.
At least 38 people were killed in sprawling Uttar Pradesh state, which has a population of more than 210 million people, said government spokesman Avnish Awasthi. More details are awaited.
A heavy dust storm and rain hit a number of other parts of the country including capital Delhi and the National Capital Region on Sunday. Two deaths were also reported in Delhi.
President Ram Nath Kovind and Prime Minister Naremdra Modi expressed grief over the loss of lives in weather related incidents. the President in a tweet said, "Sad to hear of loss of lives due to rain and thunderstorms in different parts of the country". Condolences to the bereaved families.
The hill states of Jammu and Kashmir, Himachal Pradesh and Uttarakhand in the north and Meghalaya, Nagaland, Manipur, and Tripura in the northeast are also likely to receive rainfall and thunderstorm. "Asked officials to provide all possible assistance to those affected".