The storm, known internationally as Kai-Tak, was expected to reach the extreme northern part of the island Wednesday, the Philippine Daily Inquirer reported.
From there, the typhoon was expected to affect southern Taiwan.
The two killed were from the provinces of Pangasinan and Ilocos Norte, the National Disaster Risk Reduction Management Council said Tuesday afternoon.
Typhoon Helen had maximum sustained winds of 52.8 mph with gusts up to 62 mph, the Philippine Atmospheric, Geophysical and Astronomical Services Administration said. The storm had a diameter of 310 miles and heavy rain was falling at up to 1.4 inches an hour.
The center of the storm was last reported 143 miles east-northeast of Tuguegarao City and was expected to move northeast at 8 mph, the weather service said. The northern Philippines had already been hit by deadly flooding that displaced hundreds of thousands of people.
The death toll from two weeks of torrential rains reached 95 Tuesday, GMA News reported, quoting the disaster management council. That includes 69 drowning deaths and another 12 in landslides. At least four people remain missing.
The council said torrential rains had affected about 3.45 million people. About 342,000 were in 810 evacuation centers, while others were returning to their homes as the waters subsided.