The fatality, a man in his 50s, was electrocuted while wading in floodwaters in Lingig town, in Mindanao's Surigao del Sur province, according to Johnny Pimentel, the provincial governor.
"One person was electrocuted due to downed electric posts," Governor Pimentel told Xinhua by mobile phone.
He said rain has already stopped in most of the province as of 9 am Friday.
Surigao del Sur was placed under public storm signals since Thursday as the typhoon was nearing the province's coastal town of Hinatuan.
After first hitting land around 4:30 am local time in Guiuan town, in Eastern Samar province early Friday, the storm intensified further up to 275 kilometer per hour of gusts as it made its second landfall in Tolosa town, Leyte more than two hours later, said the Philippine Atmospheric, Geophysical and Astronomical Services Administration.
Disaster and weather authorities warned about widespread destruction in areas on the storm's path, with uprooted trees, downed power lines and houses already sustaining damage in Samar- Leyte areas.
The Philippines, being at the Typhoon Belt between Pacific Ocean and the South China Sea, is visited by an average of up to 22 storms yearly.