We present a method for measuring the shear complex modulus of hydrogels by oscillatory nanoindentation, with unprecedented attention to procedure and uncertainty analysis. The method is verified by testing a typical low-molecular-weight gelator formed from the controlled hydrolysis of glucono-δ-lactone. Nanoindentation results are compared with those obtained by rheometry using both vane-in-cup and parallel-plate fixtures. At 10 Hz, the properties measured by oscillatory nanoindentation were G′ = 38.1 ± 2.8 kPa, tan δ = 0.22 ± 0.02. At the same frequency, the properties measured by rheometry were G′ = 15.3 ± 2.9 kPa, tan δ = 0.11 ± 0.016 (vane-in-cup) and G′ = 7.9 ± 1.1 kPa, tan δ = 0.05 ± 0.004 (parallel-plate). The larger shear modulus measured by nanoindentation is due to the scale of testing. Whereas rheometry characterizes the bulk material response, nanoindentation probes the fibrous network of the gel. The procedure and analysis presented here are valuable for nanoindentation testing of other compliant materials such as hydrogels, soft biological tissue, and food products.