In indoor environments, estimating localization using a received signal strength indicator (RSSI) is difficult because of the noise from signals reflected and refracted by walls and obstacles. In this study, we used a denoising autoencoder (DAE) to remove noise in the RSSI of Bluetooth Low Energy (BLE) signals to improve localization performance. In addition, it is known that the signal of an RSSI can be exponentially aggravated when the noise is increased proportionally to the square of the distance increment. Based on the problem, to effectively remove the noise by adapting this characteristic, we proposed adaptive noise generation schemes to train the DAE model to reflect the characteristics in which the signal-to-noise ratio (SNR) considerably increases as the distance between the terminal and beacon increases. We compared the model’s performance with that of Gaussian noise and other localization algorithms. The results showed an accuracy of 72.6%, a 10.2% improvement over the model with Gaussian noise. Furthermore, our model outperformed the Kalman filter in terms of denoising.