The developing brain employs multi-step processes to construct neural circuitry. Recent studies have highlighted that microglia, traditionally known to be the resident immune cells in the brain, have essential roles in these processes, which range from neurogenesis to establishing synaptic connections. Microglia play bidirectional roles for maintaining proper circuitry: eliminating unnecessary cells, axons, and synapses, while supporting the neighboring ones. Although these processes are performed in different parts of the neuron, similar molecular mechanisms are possibly involved. This paper reviews recent progress on the knowledge of the roles of microglia in brain development, and further discusses the application of this knowledge in therapies for brain disorders and injuries.