Abstract: To overcome the performance limitation of multipath time-delay estimation posed by underwater acoustic sinusoidal signals, a novel approach incorporating the frequency-domain weighting of the highly oscillatory Nonlinear Least Squares (NLS) cost function with the evolutionary optimization is proposed in this paper to facilitate the accurate estimation of the multipath time-delay of sinusoidal signals. In the described method, the number of the effective multipath signals, which is included into the parameter model as well as the multipath time-delay and amplitude factor, can be estimated simultaneously thus avoiding the requirement of additional computation. Experimental results performed with numerical simulation and sea-trial data are provided, demonstrating the effectiveness and precision enhancement of the proposed algorithm.