I should start off by saying that it seems like the popular idea of the Middle Ages is that people got raped all the time...like Game of Thrones is supposed to be gritty realism and all the rape is “just how it was”. Well it probably wasn’t happening constantly, but it did happen, and like today, it was a serious crime.

Sometimes it can be difficult to write about pre-modern sexual assault because we don’t have the sources we need - women did not write very much in general, especially in the 12th century (which is relatively early, in terms of women writing).

There is a ton of fictional medieval literature where rape occurs though, so even if it didn’t happen constantly, it was clearly something people were worried about and something they took very seriously.

On the legal side, it helps that your question already narrows it down to the 12th century, and we can narrow it even further to 12th-century England.

In medieval England, there was a pretty well-developed legal structure. The king would periodically send out judges to deal with legal matters throughout the kingdom (“itinerant justices”). This was as true for the major nobles of the kingdom as it was for the lowliest peasants - one set of laws applied to everybody, and every one of his subjects was entitled to the king’s justice (at least in theory).

But if you’re a peasant in a village, and the people in your village accused you of rape, you would just be living there alongside them until the judges arrived. Judges wandered around the country all year and people brought cases to them when they arrived. They had no authority to make arrests on their own, so it was up to the victims of the crimes to bring the accused before them.

The accusers would present their evidence to the judges. It would certainly be harder to prove if there were no witnesses, as mentioned in the question. Did you leave any physical evidence behind? (Obviously not DNA evidence yet - but did the victim fight back and injure you?) Did you talk about it to someone else beforehand, or tell someone about it afterwards? You could testify on your own behalf as well, and either admit you did it, or deny it. You could swear an oath that you were innocent, maybe on a Gospel book or some saints’ relics. Your accuser and the judges could simply accept that, assuming you wouldn’t lie when swearing a solemn oath, or they could find you guilty.

The trial could be more like an arbitration than a modern criminal trial. Usually, for rape and for any other crime, the punishment was a fine. The amount of money depended on the social standing of the victim and the seriousness of the crime, but everyone and everything had a price. Although if the crime was sufficiently bad, you could be executed.

This just applies to England though. In 12th-century France, it didn’t work like this because the king only controlled a small area around Paris. In Normandy or Brittany or Aquitaine, or in the smaller counties and lordships within those territories, the local lords were responsible for administering justice, and their methods for dealing with rape could be much different. Elsewhere in Europe your punishment might also depend on the whims of the local lords or your neighbours. In that case, if you were accused of rape you might be killed extra-judicially (i.e. the victim’s family might come after you), or castrated, or just chased out of the village, or they might think of some other creative way of punishing you.

Technically anything involving sex could also be dealt with under church law (canon law). Under canon law you couldn’t be executed, so the worst punishment for rape was excommunication. The church wasn’t very concerned with peasants, who would be subject to secular law, but it would get involved if someone raped a nun (an extremely serious crime for the church). It was also very interested in what we might call “statutory” rape, which was probably what rape was most of the time. Anyone who isn’t supposed to be having sex, according to the church (an unmarried woman, for example, or really any premarital sex, as we would call it) could be considered to have been raped.

So, your most likely outcome, if you were a peasant in 12th-century England, was that you’d be convicted by the king’s itinerant judges, and would have to pay a fine; elsewhere, you might suffer a more creative punishment or be killed; and if the church was involved you could be excommunicated.

The sources for this are pretty vast. A lot has been written about rape in medieval literature as well, and how it relates to rape in the real world. Here is a very small sample of sources about peasants, women, the law, and literature:

Paul R. Hyams, King, Lords and Peasants in Medieval England: The Common Law of Villeinage in the Twelfth and Thirteenth Centuries (Clarendon Press, 1980)

James A. Brundage, Law, Sex, and Christian Society in Medieval Europe (University of Chicago Press, 1987)

Kathryn Gravdal, Ravishing Maidens: Writing Rape in Medieval French Literature and Law (University of Pennsylvania Press, 1991)

Barbara A. Hanawalt, ‘Of Good and Ill Repute’: Gender and Social Control in Medieval England (Oxford University Press, 1998)

Noel J. Menuge, ed., Medieval Women and the Law (Boydell, 2000)

Phillipp R. Schofield, Peasant and Community in Medieval England, 1200-1500 (Macmillan, 2003)

Caroline Dunn, Stolen Women in Medieval England (Cambridge University Press, 2013)