The 64-year-old rocker has reportedly been making secret trips between the US and Germany over the last five years to receive radiation treatment to keep the disease in check.
According to TMZ, Eddie - who was a heavy smoker - believes he contracted the disease as a result of a metal guitar pick which he used to use as he would cradle it in his mouth.
Eddie was diagnosed with tongue cancer in 2000 and had around 1/3 of the muscle removed.
Sources told the publication that since then, there were times when some of the cancer cells migrated down to his throat and doctors would scrape them out.
The 'Jump' hitmaker is said to currently be "doing OK".
Eddie has previously spoken of his theory that his use of metal guitar picks caused his cancer.
He said in 2015: "I used metal picks - they're brass and copper - which I always held in my mouth, in the exact place where I got the tongue cancer.
"Plus, I basically live in a recording studio that's filled with electromagnetic energy. So that's one theory. I mean, I was smoking and doing a lot of drugs and a lot of everything. But at the same time, my lungs are totally clear. This is just my own theory, but the doctors say it's possible."
The rocker's friend, Toto guitarist Steve Lukather previously claimed "health issues" were stopping Van Halen - Eddie, his brother, drummer Alex Van Halen, his son, bassist Wolfgang Van Halen and singer David Lee Roth - from getting out on the road.
He also said recently: "I love Ed and Alex, they've been friends of mine for 40 years.
"Everybody wants Van Halen back -- nobody more than me, because I still think they're one of the greatest rock and roll bands of all time. Eddie changed the planet.
"Him and Alex are sitting there laying back and they're waiting to see what happens next. I think they're on a hiatus."