You know, the western Middle Ages invented modern anti-Semitism. They incubated our concept of racism, introduced pogroms against Jewish communities, kicked mass populations of Muslims out of their homes, put pigs on trial for murder, thought public execution was popular entertainment, approved of rape and enslavement as logical and necessary payment for soldiers, started burning people at the stake for having same-sex sex, had a tiny warrior caste that burned and looted the homes of everyone else and if they died oh well, and reacted to outbreaks of disease by starving and beating themselves.

I don’t care how transphobic or feminist you are, the European Middle Ages are NOT your evidence to argue one way or the other about gender and sex roles.

First: yes, there absolutely were different words for boy and girl. We can start with Latin puer and puella, in which—as usual—in a mixed gender group, girls were subsumed into pueri. You might also see divisions between “sons” and “daughters”—I get knebelin and tochterlin in the texts I read (Middle High German) a lot, in addition to the generic kindelin. (The -lein is a diminutive to signify ‘little’, more or less).

Yes, it mattered at birth. Jewish fathers circumcised their infant sons; there was no equivalent for daughters. Meanwhile, Christian and very anti-Semitic poet/printer/barber/surgeon/what-have-you Hans Folz write a poem of advice for men of the urban bourgeoisie. He describes the expectant father waiting outside the birth chamber, pacing, nervous, excited—and wanting to know “whether the baby will be a he or a she.”

(As Butler points out, we perform sex as well as gender.)

Moving into toddlerhood, distinctions continue. Yes, it was the responsibility of mothers (in general) to raise little children; generally the age here is 7, normatively; who know what it amounted to in practice but that’s our rough guide. But that in no way portends a lack of gender roles in medieval Europe any more than having a stay at home mom or dad does today. Right away, toys are gendered. In addition to generic balls, hoops, &c, boys play with miniature versions of adult male paraphernalia—swords being the most common. Archaeological evidence shows us girls playing with kid-sized pots and pans, essentially playing House.

Cities heighten the distinction, including kids from the countryside moving to cities. Bourgeois girls and boys had VERY different opportunities for education, to the point where the rise of vernacular literature and literacy is in large part seen as a function of women reading.

But make no mistake: when the printing press gets going in late 15C, the second most popular—read: profitable—genre to print is Latin grammar textbooks. Outside monasteries, Latin means specifically education for boys.

Rich girls in the late Middle Ages did have some opportunities for literate education even outside being marked as a future nun, but they were much more rare, and often informal. (Formally, we know of civic schools in vernacular education for girls in cities like Nuremberg, and some parish schools for girls and boys in England).

Even medieval people had begun to grasp that this division of education was a social concept and unfair, not inherent. 14th-15th century early humanist Christine de Pizan wrote, among a billion other things including a military manual, a treatise whose point was in part, women are every bit the intellectual equals of men; they just are deprived of equal access to book-education.

Lower-class children in cities tended to work as domestic servants. Boys might work in a shop, girls in the home.

I want to be clear that every single one of these things is a social construction. The division into just two groups (daughters and sons, he and she), the toys set up to resemble adulthood, religious rituals, education access, work. Nevertheless, they were absolutely deployed in practice, not just normative.

One way or the other, the European Middle Ages are not the place from which to make arguments about inherent or “objective” gender/sex.

I see that, while I was writing, /u/sunagainstgold wrote up a much better discussion of the broader issues of gender here. So I'll just comment briefly on the terminology in the article in question:

It doesn't seem to me that that article is actually saying that 'girl' was the only way to refer to both boys and girls, just that neither 'boy' nor 'girl' meant what they do today in Middle English. Even if that were the case, I'm not sure what the problem would be, since it notes that terminology still existed to distinguish male and female children in ‘knave girls’ and ‘gay girls’ or ‘knave child’ and ‘maiden child’. (The latter of which are evidently descended from Old English compounds like cnihtcild/hysecild and mægdencild/wífcild for boy and girl respectively.)

Its point about 'boy' and 'girl', more generally, is not incorrect. The OED notes that the word 'girl' is attested back to 1300 as referring to: "A child of either sex; a young person" noting as the article does that "knave girl" refers to "a boy". Likewise in reference to women it also notes that: "gay girl" is frequent in early sources. (The earliest attestation they give of 'girl' alone referring to a woman is ?1520 and 1546.) The OED also notes of 'boy' that from 1300 it also means: "A male servant, slave, assistant, junior employee". Although it notes it as a term of abuse for lowborn boys from the same period, and unambiguous references to male children from 1440.

Of course, there were plenty of other languages used in the Middle Ages. As sunagainstgold notes, puer and puella mean roughly 'boy' and 'girl' in Latin. These are attested in the Dictionary of Medieval Latin from British Sources in this sense across every period of the middle ages. Likewise in Ælfric's glossary, from around the turn of the second millennium, we find these terms glossed as puella -> mǣden and puer -> cild.

But, to once again underscore sunagainstgold's point, just because they have the terminology for these things, it doesn't mean that they meant exactly the same thing as we do by this terminology. For example, male children in Latin are taken as something of a default. We see this immediately in the gloss of puer as cild, as this reflects very accurately the way that in puer can be used to simply mean child. For example, it or the derived abstract noun pueritia are very often used as the second age of man, after infancy (infantia) and before adolescence (adolescentia).