High-frequency components are often discarded for data denoising when applying pure wavelet multiscale or empirical mode decomposition (EMD) based approaches. Instead, they may raise the problem of energy leakage in vibration signals. Hybrid EMD and wavelet packet (EMD-WP) is proposed to denoise Global Positioning System-(GPS-) based structure monitoring data. First, field observables are decomposed into a collection of intrinsic mode functions (IMFs) with different characteristics. Second, highfrequency IMFs are denoised using the wavelet packet; then the monitoring data are reconstructed using the denoised IMFs together with the remaining low-frequency IMFs. Our algorithm is demonstrated on a synthetic displacement response of a 3-story frame excited by El Centro earthquake along with a set of Gaussian random white noises on different levels added. We find that the hybrid method can effectively weaken the multipath effect with low frequency and can potentially extract vibration feature. However, false modals may still exist by the rest of the noise contained in the high-frequency IMFs and when the frequency of the noise is located in the same band as that of effective vibration. Finally, real GPS observables are implemented to evaluate the efficiency of EMD-WP method in mitigating low-frequency multipath.