Three-dimensional cell culture and the forming multicellular aggregates are superior over traditional monolayer approaches due to better mimicking of in vivo conditions and hence functions of a tissue. A considerable amount of attention has been devoted to devising efficient methods for the rapid formation of uniform-sized multicellular aggregates. Microfluidic technology describes a platform of techniques comprising microchannels to manipulate the small number of reagents with unique properties and capabilities suitable for biological studies. The focus of this review is to highlight recent studies of using microfluidics, especially droplet-based types for the formation, culture, and harvesting of mesenchymal stem cell aggregates and their subsequent application in stem cell biology, tissue engineering, and drug screening. Droplet-based microfluidics can be used to form microgels as carriers for delivering cells and to provide biological cues to the target tissue so as to be minimally invasive. Stem cell-laden microgels with a shape-forming property can be used as smart building blocks by injecting them into the injured tissue thereby constituting the cornerstone of tissue regeneration.