Falasteen Al-Ryadi's Ayman Alkurd, who plays for the Palestinian national team, Shadi Sbakhe of Khadamat Alniserat and the 24-year-old Wajeh Moshtahe of Gaza's Ittihad Alshojaeya were in their homes when they died.
Rafah's stadium, where one of Palestinian football's leading clubs, Ahli Alenserat, trains, was also seriously damaged during the Israeli offensive, which entered its 19th day on Wednesday, the news agency said.
The Palestinian national football team was ranked 180 out of 207 in FIFA World Ranking in January.
The Haaretz newspaper reported on Wednesday that the Israel Football Association has decided to resume nationwide matches this weekend after a three-week winter break and a one-week pause due to the military operations in Gaza. The paper said games were still barred from being held in Arab communities.
The death toll in Gaza since December 27, when Israel first launched airstrikes on the enclave, is reported to have risen to over 920, with half of the dead civilians, while more than 4,000 have been injured.