Here's what Wikipedia says about its origin:

"The origin of this gesture is highly speculative, but is quite possibly up to 2500 years old. It is identified as the digitus impudicus ('impudent finger') in Ancient Roman writings [1] and reference is made to using the finger in the Ancient Greek comedy The Clouds by Aristophanes. It was defined there as a gesture intended to insult another. It has been noted that the gesture resembles an erect penis.

Ancient Romans also considered an image of an erect phallus as a talisman against evil spells. As a consequence, displaying this gesture to another may not have been a pseudo-sexual insult but rather an insulting statement along the lines of—"I'm going to protect myself against your witchcraft, before you even start" but an even earlier reference is made to ancient farmers using this finger to test hens for coming eggs.

Jean Froissart (circa 1337-circa 1404) was a historian and the author of Froissart's Chronicles, a document that is essential to an understanding of Europe in the fourteenth century and to the twists and turns taken by the Hundred Years' War. The story of the English waving their fingers at the French is told in the first person account by Jean Froissart. However, the description is not of an incident at the Battle of Agincourt, but rather at the siege of a castle nearby in the Hundred Years' War. Adding to the evidence is that by all accounts Jean Froissart died before the battle actually took place; it was therefore rather difficult for him to have written about it.

One should note that Jean Froissart's writings aren't the most reliable and that a similar story is told about the English giving the V sign. This can be further looked into at the Battle of Agincourt."

The article on the Battle og Agincourt says this:

"It has long been told that the famous "two-fingers salute" and/or "V sign" derives from the gestures of English archers, fighting at Agincourt. The myth claims that the French cut off two fingers on the right hand of captured archers and that the gesture was a sign of defiance by those who were not mutilated.

This may have some basis in fact - Jean Froissart (circa 1337-circa 1404) was a historian as the author of The Chronicle, a primary document that is essential to an understanding of Europe in the fourteenth century and to the twists and turns taken by the Hundred Years' War. The story of the English waving their fingers at the French is told in the first person account by Froissart, however the description is not of an incident at the Battle of Agincourt, but rather at the siege of a castle in another incident during the Hundred Years War. Also, Froissart is known to have died before the Battle of Agincourt. If it was used at Agincourt, it was not invented there."

Eh, like everything, the origin can be debated.