Caenorhabditis elegans is a widely used model organism to study development, aging and behavior. Many of these biological studies require staging a large number of worms to assay a synchronized population of animals. Conventional synchronization techniques such as manual picking, gravity stratification and chemical bleaching are labor-intensive and could perturb animals’ physiology. Thus, there is a need for a simple inexpensive technology to sort a mixed population of worms based on their developmental stages with minimal perturbation. Here we demonstrate a simple but accurate and high-throughput technique to sort based on animal size, which correlates well with developmental stages. The device consists of an array of geometrically optimized pillars that act as a sieve to allow worms of specific sizes to rapidly move through. With optimized chamber heights, pillar spacing and driving pressures, these binary separation devices are capable of independently separating a mixture of worms at two different stages at average efficiency of around 95%, and throughput of hundreds of worms per minute. In addition, when four devices are used sequentially, we demonstrate the ability to stratify a mixture of worms of all developmental stages with >85% overall efficiency.