Did it happen? Absolutely. Was it legally and socially condoned on a broad scale? No, it was not. Sexual relations with boys was one of the behaviors that early Christian and later medieval Christian authorities desired to root out, both due to its association with non-Christian cultures and on its own merits so to speak, and it fell within the parameters of the criminalization of sodomy. (Whether legitimately or as an everything-and-the-kitchen-sink approach to accusations, chroniclers and courts often attached sodomy to other charges of misconduct or heresy -- this might be useful to bear in mind if you're trying to contextualize accusations of fornication with boys and/or between men aimed at religious sects or political organizations in this period.) A large part of what we know about sexual relations between adults and male children is drawn from legal records -- disciplinary records within religious organizations, court records drawn from trials for sodomy, and so on. Like modern child sexual abuse, the vast majority of sexual actions by adults toward children likely never made it to court; sodomy laws might be broad or specific, and they might differentiate between the younger party as less culpable/not culpable for their treatment or they might not. But from this we can still draw a picture of how and when these events occurred.

Sexual conduct between adult men and boys occurred in institutional contexts -- within the Church and within monastic life where adult monks might have access to adolescent novices or child oblates. It occurred in a community context -- within families and neighborhoods, by teachers toward students, and so on. It occurred in an employment-based context, such as the sexual abuse of apprentices and servants by their masters and employers, or of younger laborers by older laborers. It was facilitated by the imbalances of power that are endemic in these contexts and where adult men have access to young boys. While sexual contact between men and boys might be winked at or informally condoned in certain contexts, it was not enshrined as broadly socially acceptable within medieval Europe in the way one might think of when you're thinking of ancient Greek pederasty.

There's a scanty but present body of works written in the Middle Ages (generally by clerical writers) that romanticize relationships between men and boys, or that eroticize younger men -- this is at a contrast with the larger body of writings from the Muslim world or from the Classical Greek and Roman world. Some of it draws on Classical literary conventions like pastoral literature, other work draws on the conventions of vernacular love poetry. This was not the main line of poetry at this time or a broadly socially-accepted genre.

(For medieval homoerotic pastoral poetry where the object of desire is implicitly/explicitly younger, Rictor Norton's outline of homoerotic pastoral poetry after the Classical period but before the Renaissance outlines some, though I disagree with some of his assertions about some specific writings and in general due to Norton's focus on the history of homosexuality, versus the specific history of same-sex sexual acts between men and boys, some material gets conflated that's outside the scope of OP's question. In general I really like Norton for primary sources, but a lot of his commentary makes me suck my teeth a little.)