A 51-year-old man died when a wall collapsed on him in the village of Razvigorovo, near the eastern town of Shumen, the interior ministry said.
The second victim was a 67-year-old man from the town of Veliki Preslav, in the same region, it added.
He was believed to to have walked on a broken electricity cable while herding his sheep back home in the storm. Two of his animals also died in the accident.
A woman was also hospitalised after a tree fell on her in a public garden at Shumen.
Hundreds of firefighters, rescuers and police responded to calls over damage caused by the heavy rains and gusting winds on Saturday.
The southern region of Smolyan as well as the regions of Targovishte, Razgrad, Silistra and Shumen, to the north east, suffered the most serious damage, the ministry said.
The storm damaged roofs and toppled trees and electricity poles, prompting electricity outages in several dozen villages across the country.
The eastern town of Devnya declared a partial state of emergency after the storm.
The new weather extremes come just two months after four people died in torrential rains that flooded parts of Bulgaria's Black Sea coast, cutting bridges and leaving thousands of tourists stranded.
At least 16 people were killed this week as Storm Ciaran hit western Europe with downpours and record winds that brought travel chaos.
Scientists warn that extreme weather is becoming more intense as a result of climate change.
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