Viscosity variation in human fluids, such as Synovial Fluid (SF) or Cerebrospinal Fluid (CSF), can be used as a diagnostic factor; however, the sample volume obtained for analysis is usually small, making it difficult to measure its viscosity. On the other hand, Quartz Crystal Resonators (QCR) have been used widely in sensing applications due to their accuracy, cost, and size. This work provides the design and validation of a new viscosity measurement system based on quartz crystal resonators for low volume fluids, leading to the development of a sensor called “ViSQCT” as a prototype for a new medical diagnostic tool. The proposed method is based on measuring the resonance frequency at the crystal’s maximum conductance point through a frequency sweep, where crystals with 10 MHz fundamental resonance frequency were used. For validation purposes, artificial fluids were developed to simulate SFs and CFs in healthy and pathological conditions as experiment phantoms. A commercial QCR based system was also used for validation since its methodology differs from ours. A conventional rotational viscometer was used as a reference for calibration purposes. ViSQCT demonstrates the capability to measure the sample’s viscosity differentiation between healthy and pathological fluid phantoms and shows that it can be used as a basis for a diagnostic method of several pathologies related to the studied biological fluids. However, some performance differences between both QCR-based systems compared to the reference system deserves further investigation.