The generation of terminally differentiated cell lineages during organogenesis requires multiple, coordinated cell fate choice steps. However, this process has not been clearly delineated, especially in complex solid organs such as the pancreas. Here, we performed single‐cell RNA‐sequencing in pancreatic cells sorted from multiple genetically modified reporter mouse strains at embryonic stages E9.5–E17.5. We deciphered the developmental trajectories and regulatory strategies of the exocrine and endocrine pancreatic lineages as well as intermediate progenitor populations along the developmental pathways. Notably, we discovered previously undefined programs representing the earliest events in islet α‐ and β‐cell lineage allocation as well as the developmental pathway of the “first wave” of α‐cell generation. Furthermore, we demonstrated that repressing ERK pathway activity is essential for inducing both α‐ and β‐lineage differentiation. This study provides key insights into the regulatory mechanisms underlying cell fate choice and stepwise cell fate commitment and can be used as a resource to guide the induction of functional islet lineage cells from stem cells in vitro. Synopsis Combining genetic lineage tracing and single‐cell gene expression analyses, this resource deciphers the multistep trajectories of endocrine and exocrine lineages and intermediate progenitor populations during early murine pancreas development. Single‐cell analysis of cell lineages from fetal pancreas at E9.5–E17.5 identifies differentiation steps and pathways from multipotent progenitors to endocrine and exocrine lineages. Fifteen cell clusters delineate all pancreatic cell types and four steps of cell fate decisions from progenitors to islet lineages. Developmental pathways involved in the “first wave” of alpha‐cell generation differ from intermediate progenitor and population specific markers. Endocrine progenitors undergo four transient stages. The MAPK/ERK pathway restrains early endocrine specification. An integrated analysis defines specification of pancreatic cell types from multipotent progenitors to endocrine and exocrine lineages and branching points during early mouse development.