Provided is an apparatus and method for controlling a droplet. The apparatus for controlling the droplet does not contaminate/damage a sample, has a high degree of freedom in droplet control, and is capable of being repeatedly used for a long time. An apparatus (100) for controlling a droplet according to an embodiment includes a flexible substrate (120) having a hydrophobic or oleophobic surface, a dimple formation unit (140), which locally deforms a bottom surface of the flexible substrate (120) to form a dimple, and a driving unit (160), which moves the dimple formation unit (140) at a lower side of the flexible substrate.