This paper presents a new algorithm for adaptive resampling, called percentile-based resampling (PBR) in a sequential Bayesian filtering, i.e., particle filter (PF) in particular, to improve tracking quality of the frequency trajectories under noisy environments. Since the conventional resampling scheme used in the PF suffers from computational burden, resulting in less efficiency in terms of computation time and complexity as well as the real time applications of the PF. The strategy to remedy this issue is proposed in this work. After state updating, important high particle weights are used to formulate the pre-set percentile in each sequential iteration to create a new set of high quality particles for the next filtering stage. The number of particles after PBR remains the same as the original. To verify the effectiveness of the proposed method, we first evaluated the performance of the method via numerical examples to a complex and highly nonlinear benchmark system. Then, the proposed method was implemented for frequency estimation for two time-varying signals. From the experimental results, via three measurement metrics, our approach delivered better performance than the others. Frequency estimates obtained by our method were excellent as compared to the conventional resampling method when number of particles were identical. In addition, the computation time of the proposed work was faster than those recent adaptive resampling schemes in literature, emphasizing the superior performance to the existing ones.