According to the Guardian Fallon has recently come under fire and apologised earlier this week for putting his hand on a journalist's knee in 2002.
It was already reported that he would face no investigation for this as the woman in question laughed it off.
However, it is unclear if any further allegations may have prompted his resignation.
Fallon is the first politician to step down in a developing scandal at Westminster. A number of allegations have surfaced about Member of Parliament (MPs) in recent days.
In his resignation letter to U.K. Prime Minister Theresa May, Fallon said, "A number of allegations have surfaced about MPs in recent days, including some about my previous conduct." Adding, "Many of these have been false but I accept in the past I have fallen below the high standards that we require of the armed forces that I have the honour to represent."
"I have reflected on my position and I am now resigning as defence secretary," Fallon said.
In her response, May thanked him for his service.
"I appreciate the characteristically serious manner in which you have considered your position, and the particular example you wish to set to servicemen and women and others," she said.
May is expected to appoint a replacement on Thursday. (ANI)