In the High Middle Ages, new sources of education arose. Choir and grammar schools were designed to train priests, with an emphasis respectively on music and Latin grammar. The reorganisation of the church that began in the reign of David I (1124-53) gave the church a clearer diocesan and parochial structure, meaning that the seats of sheriffdoms, such as Perth, received schools that were usually under monastic patrons. Early examples of grammar schools include the High School of Glasgow in 1124 and the High School of Dundee in 1239. These were usually attached to cathedrals or a collegiate church. The newly created diocesan chancellors may have had authority over cathedral schools and schoolmasters within their diocese.
The new religious orders that became a major feature of Scottish monastic life in this period also brought new educational possibilities and the need to train larger numbers of monks. Benedictine and Augustinian foundations probably had almonry schools, charity schools using funds from the almoner to provide a type of bursary to educate young boys, who might enter the priesthood. At the Cluniac Paisley Abbey, secular chaplains were employed as schoolmasters. Some monasteries, including the Cistercian abbey at Kinloss, Sweetheart Abbey and Beauly, opened their doors to a wider range of students to teach the sons of gentlemen. St Andrews, which was both the seat of a bishop and the site of a major Augustinian foundation, had both a grammar school, under the archdeacon, and a song school, under the priory. The foundation of over 100 collegiate churches of secular priests between 1450 and the Reformation would have necessitated the training of large numbers of choristers. Sometimes, as at Lochwinnoch, they were taught both music and grammar. Dominican friars were noted for their educational achievements and were usually located in urban centres, probably teaching grammar, as at Glasgow and Ayr. The number and size of these schools seems to have expanded rapidly from the 1380s. By the end of the Middle Ages, grammar schools could be found in all the main burghs and some small towns.
Educational provision was probably much weaker in rural areas, but there were petty or reading schools that provided an elementary education. There was also the development of private tuition in the families of lords and wealthy burghers. Sometimes these developed into "household schools", that may also have catered to neighbours and kin, as well as the sons of the laird's household, which is known to have happened at Huntly. All these schools were almost exclusively aimed at boys. Girls of noble families were taught in nunneries such as Elcho, Aberdour and Haddington. By the end of the fifteenth century Edinburgh also had schools for girls, sometimes described as "sewing schools", whose name probably indicates one of their major functions. Although reading may also have been taught in these schools, the students were probably taught by lay women or nuns.
There is documentary evidence for about 100 schools of these different kinds before the Reformation. Most of the schoolmasters of these schools were clergy, and also acted as chaplains of religious foundations, hospitals or private chaplains of noblemen to supplement their merge incomes. To some extent, all education was controlled by different branches of the church, but towards the end of the period there was an increasing lay interest. This sometimes resulted in conflict, as between the burgh of Aberdeen and the cathedral chancellor, when the former appointed a lay graduate as schoolmaster in 1538, and when a married man was appointed to the similar post in Perth. Education began to widen beyond the training of the clergy, particularly as lay lawyers began to emerge as a profession, with a humanist emphasis on educating the future ruling class for their duties. The growing humanist-inspired emphasis on education cumulated with the passing of the Education Act 1496, thought to have been steered through parliament by the Keeper of the Privy Seal William Elphinstone, Bishop of Aberdeen, which decreed that all sons of barons and freeholders of substance should attend grammar schools to learn "perfyct Latyne". All this resulted in an increase in literacy, which was largely concentrated among a male and wealthy elite, with perhaps 60 per cent of the nobility being literate by the end of the period.