N6-methyladenosine (m6A) is an RNA modification that affects RNA stability, localisation and translation. It is most common in the brain where it directs critical neurodevelopmental processes such as neurogenesis, axon guidance and synaptogenesis. However, m6A patterns are complex and can differ between alternative isoforms. Therefore, understanding m6A functions requires an isoform-level map. Despite its known importance and complexity, m6A has not been profiled at the isoform-level in the developing human brain. We aimed to analyse m6A in cortical brain organoids, the gold-standard model of early brain formation, using Nanopore Direct RNA Sequencing (DRS), to produce a high-resolution m6A map across two distinct neurodevelopmental timepoints. We detected 101,810 unique m6A sites across 15,495 isoforms. More than 3,000 transcriptomic locations had sizeable and significant differences in modification rates between early (1-month) and late (4-month) cortical organoids, with a greater number of significant increases found at 4-months. Yet contrary to previous literature, m6A site numbers and modification levels were not globally higher in later development. Additionally, single-nucleotide isoform-level resolution of m6A stoichiometry revealed concordant m6A rate changes between modification sites on individual isoforms and an unexpected positive correlation between the number of m6A sites on an isoform and average modification rates. Thus, the difference between global and isoform-level m6A distributions in this study demonstrates the importance of isoform-level analysis. Utilising our high-resolution isoform-level insights, future work will be better-equipped to elucidate functional roles of specific m6As and/or m6A-modified isoforms, with implications for our understanding of neurological development and disease. More broadly, these novel m6A findings will inform epitranscriptomic research beyond brain development.