The Caenorhabditis elegans embryo is a widely used model for the functional analysis of dynamic cellular processes, such as chromosome segregation, cytokinesis or lineage analysis. However, the conventional embryo preparation method that relies on manually dissecting gravid worms to extract embryos is somewhat time consuming and does not lend itself to high throughput assays. Here, we report a fully integrated microfluidic approach for C. elegans early embryogenesis assays with unprecedented accuracy and throughput. The device consists of a compressible microfluidic pillar-array chamber for robust and fast on-chip extraction of embryos from the uterus of gravid nematodes. Subsequently, embryos are immobilized by automated fluidic transfer in a microtrap array for individual tracking of a large number of embryos, including fragile mutants with drug-permeable eggshells. Our device allows high-resolution live imaging of very early events in embryogenesis, starting from the one-cell stage. We also demonstrate the feasibility of well-controlled compound application in versatile microfluidic pharmacological assays performed on early embryos.