Generally, mesoporous silica materials, such as SBA-15, are hydrothermally synthesized in batch reactors. We synthesized SBA-15 in a dropwise flow reactor, which has several merits, such as short reaction times, continuous operation, and easy scale-up. The reaction system had three parts: a mixer and two reaction channels, one operated at a low temperature of 35 °C for the self-assembly of 2D hexagonal silica structures, and the other operated at a high temperature of over 80 °C to increase the stability of the silica structure. Two different operating schemes were used to mix the two immiscible reactant streams, one with a magnetically driven active mixer and the other with a direct supply of premixed reactants. The dropwise flow reactor with the active mixer instead of the low-temperature reaction channel produced fractured silica particles in the final product. However, when a premixed solution under hydrolysis conditions was employed, the synthesis of mesoporous silica SBA-15 was successful within 2.5 h in the dropwise flow reactor, showing close physical properties to the reference SBA-15 sample obtained in a conventional batch reactor.