Origins
The word 'lesson' enters English from Old French 'leçon,' itself from Latin 'lectiōnem' (accusative of 'lectiō'), meaning 'a reading aloud, a passage read.' The Latin noun derives from 'lectus,' the past participle of 'legere,' one of the most semantically rich verbs in the Latin language. 'Legere' meant simultaneously 'to read,' 'to gather,' 'to collect,' and 'to choose' — senses that may seem unrelated until one considers that early reading was literally the gathering of letters into words, and that choosing ('selecting') involves picking things out from a gathered set.
The PIE root behind 'legere' is *leǵ- (to gather, to collect), which produced an extraordinary family of English words. Through Latin, it gave us 'lecture' (a reading aloud), 'legend' (something that is to be read), 'legible' (capable of being read), 'elect' (to choose out), 'select' (to choose carefully), 'collect' (to gather together), 'intellect' (inter- + legere, 'to choose between,' hence 'to understand'), 'diligent' (dis- + legere, 'to single out,' hence 'careful'), and 'negligent' (nec- + legere, 'not to pick up,' hence 'careless'). Through Greek 'légein' (to say, to gather), the same root produced 'logic,' 'logos,' 'dialogue,' 'analogy,' and '-logy' (the suffix meaning 'study of'). Few roots in any language have been as productive.
The specific path from 'a reading' to 'a lesson' runs through the medieval Christian liturgy. In the early church, portions of scripture were read aloud during services, and these readings were called 'lectiōnēs.' A 'lectiō' was a passage from the Bible appointed to be read on a particular day — the congregation heard it, absorbed its moral teaching, and carried the instruction into daily life. The 'lesson' was thus originally what the priest read to you from scripture.
Middle English
Old French 'leçon' inherited both the liturgical sense (a scripture reading) and the broader educational sense (a unit of instruction). When the word crossed into Middle English around 1225, it carried both meanings. The liturgical sense survives in Anglican usage, where the 'first lesson' and 'second lesson' are the Old and New Testament readings at Matins and Evensong. The educational sense — a period of teaching, a unit of instruction — became dominant in secular contexts.
The metaphorical extension to 'a moral lesson' or 'a lesson learned from experience' appeared early, by the fourteenth century. This sense preserves the original equation between hearing a reading and absorbing its wisdom: life 'reads' you a passage, and you are expected to learn from it. 'To teach someone a lesson' — meaning to punish them instructively — dates from the seventeenth century and adds an edge of coercion to what was originally a passive act of listening.
The doublet 'lecture' entered English separately in the fourteenth century, also from Latin 'lectiō' but via a different Old French form. Where 'lesson' settled into the sense of a unit of instruction (especially at the elementary level), 'lecture' came to mean a formal discourse delivered to an audience (especially at the university level). Both words mean 'a reading' at their root, but English has specialized them into distinct registers: a child has lessons, a university student attends lectures.