Single-cell RNA-sequencing (scRNA-seq) and related technologies to identify cell types and measure gene expression in space, in time, and within lineages have multiplied rapidly in recent years. As these techniques proliferate, we are seeing an increase in their application to the study of developing tissues. Here, we focus on single-cell investigations of branching morphogenesis. Branched organs are highly complex but typically develop recursively, such that a given developmental stage theoretically contains the entire spectrum of cell identities from progenitor to terminally differentiated. Therefore, branched organs are a highly attractive system for study by scRNA-seq. First, we provide an update on advances in the field of scRNA-seq analysis, focusing on spatial transcriptomics, computational reconstruction of differentiation trajectories, and integration of scRNA-seq with lineage tracing. In addition, we discuss the possibilities and limitations for applying these techniques to studying branched organs. We then discuss exciting advances made using scRNA-seq in the study of branching morphogenesis and differentiation in mammalian organs, with emphasis on the lung, kidney, and mammary gland. We propose ways that scRNA-seq could be used to address outstanding questions in each organ. Finally, we highlight the importance of physical and mechanical signals in branching morphogenesis and speculate about how scRNA-seq and related techniques could be applied to study tissue morphogenesis beyond just differentiation.