Engineers have consistently prioritized the maintenance of structural serviceability and safety. Recent strides in design codes, computational tools, and Structural Health Monitoring (SHM) have sought to address these concerns. On the other hand, the burgeoning application of machine learning (ML) techniques across diverse domains has been noteworthy. This research proposes the combination of ML techniques with SHM to bridge the gap between high-cost and affordable measurement devices. A significant challenge associated with low-cost instruments lies in the heightened noise introduced into recorded data, particularly obscuring structural responses in ambient vibration (AV) measurements. Consequently, the obscured signal within the noise poses challenges for engineers in identifying the eigenfrequencies of structures. This article concentrates on eliminating additive noise, particularly electronic noise stemming from sensor circuitry and components, in AV measurements. The proposed MLDAR (Machine Learning-based Denoising of Ambient Response) model employs a neural network architecture, featuring a denoising autoencoder with convolutional and upsampling layers. The MLDAR model undergoes training using AV response signals from various Single-Degree-of-Freedom (SDOF) oscillators. These SDOFs span the 1–10 Hz frequency band, encompassing low, medium, and high eigenfrequencies, with their accuracy forming an integral part of the model’s evaluation. The results are promising, as AV measurements in an image format after being submitted to the trained model become free of additive noise. This with the aid of upscaling enables the possibility of deriving target eigenfrequencies without altering or deforming of them. Comparisons in various terms, both qualitative and quantitative, such as the mean magnitude-squared coherence, mean phase difference, and Signal-to-Noise Ratio (SNR), showed great performance.