N6-methyladenosine (m6A) is an abundant RNA modification that plays critical roles in RNA regulation and cellular function. Global m6A profiling has revealed important aspects of m6A distribution and function, but to date such studies have been restricted to large populations of cells. Here, we develop a method to identify m6A sites transcriptome-wide in single cells. We uncover surprising heterogeneity in the presence and abundance of m6A sites across individual cells and identify differentially methylated mRNAs across the cell cycle. Additionally, we show that cellular subpopulations can be distinguished based on their RNA methylation signatures, independent from gene expression. These studies reveal fundamental features of m6A that have been missed by m6A profiling of bulk cells and suggest the presence of cell-intrinsic mechanisms for m6A deposition. Display omitted •scDART-seq achieves global m6A profiling in thousands of single cells•Most mRNAs are methylated in a small fraction of cells•RNAs have many more m6A sites than previously reported, but most occur rarely•m6A stoichiometry is highly variable across individual cells of a population Tegowski et al. use single-cell m6A profiling to map the methylomes of thousands of individual cells. They find that m6A is highly heterogeneous at the single-cell level, with most m6A sites occurring in a small proportion of cells. They also uncover differential methylation within subpopulations of cells.