Low-flow quantiles at ungauged locations are generally estimated based on hydrological methods, such as the drainage area ratio and frequency analysis methods. In practice, the drainage area ratio approach is a popular but simple linear model. When hydrologically nonlinear characteristics govern the runoff process, the linear approach leads to significant bias. This study was conducted to develop an improved nonlinear approach using a canonical correlation analysis and neural network (CCA-NN)-based regional frequency analysis (RFA) for low-flow estimation. The jackknife technique was utilized to validate the two methods. The approaches were applied to 33 river basins in South Korea. In this work, we focused on two-year and five-year return periods. For the two-year return period, the BIAS, RMSE, and R2 were 0.013, 0.511, and 0.408 with the RFA, respectively, and −0.042, 1.042, and 0.114 with the drainage area ratio method, respectively; whereas for the five-year return period, the respective indices were −0.018, 0.316, and 0.573 with RFA, respectively, and 0.166, 0.536, and 0.044 with the drainage area ratio method, respectively. RFA outperformed the drainage area ratio method based on its high prediction accuracy and ability to avoid the bias problem. This study indicates that machine learning-based nonlinear techniques have the potential for use in estimating reliable low-flows at ungauged sites.