The elasticity of soft biological materials is a critical property to understand their biomechanical behaviors. Atomic force microscopy (AFM) indentation method has been widely employed to measure the Young's modulus (E) of such materials. Although the accuracy of the method has been recently evaluated based on comparisons with macroscale E measurements, the repeatability of the method has yet to be validated for rigorous biomechanical studies of soft elastic materials. We tested the AFM indentation method using colloidal probes and polyacrylamide (PAAM) gels of E < 20 kPa as a model soft elastic material after having identified optimal trigger force and probe speed. AFM indentations repeated with time intervals show that the method is well repeatable when performed carefully. Compared with the rheometric method and the confocal microscopy indentation method, the AFM indentation method is evaluated to have comparable accuracy and better precision, although these elasticity measurements appear to rely on the compositions of PAAM gels and the length scale of measurement. Therefore, we have confirmed that the AFM indentation method can reliably measure the elasticity of soft elastic materials.