[Object] To provide an image acquisition system, a control apparatus, and an image acquisition method that are capable of providing an appropriate image to a practitioner and an assistant by using information regarding a medical tool.[Solving Means] An image acquisition system includes: a light source unit； an imaging unit； a medical tool detection unit； and an image processing unit. The light source unit applies, to an affected part in which a medical tool that emits fluorescence by irradiation of excitation light is present, normal light and the excitation light. The imaging unit images the affected part under irradiation with the excitation light and under irradiation with the normal light, and acquires a first image signal obtained by imaging the fluorescence and a second image signal obtained by imaging the normal light. The medical tool detection unit detects, on the basis of the first image signal, an area in which the medical tool is present in a first image obtained from the first image signal. The image processing unit generates a display image using a result of detecting the area in which the medical tool is present and the second image signal.
