Real-time kinematic (RTK) positioning of the global navigation satellite systems (GNSS) is used to provide centimeter-level positioning accuracy. There are several ways to implement RTK but a Kalman filter-based RTK is preferred because of its superior capability to resolve GNSS carrier phase integer ambiguities. However, the positioning performance of the Kalman filter-based RTK is often compromised by various factors when it comes to determining a precise relative position vector between moving unmanned aerial vehicles (UAVs) equipped with low-cost GNSS receivers and antennas, where the locations of both GNSS antennas are not accurately known and change over time. Some of the critical factors that lead to a high rate of incorrect resolutions of carrier phase integer ambiguities are measurement time differences between GNSS receivers, frequent cycle slips with high noise in code and carrier phase measurements, and an improper Kalman filter gain due to a newly risen satellite. In this paper, effective methods to deal with those factors to achieve a seamless Kalman filter-based RTK performance in moving UAVs are presented. Using our extensive 45 flight tests data sets, conducted over a duration of 3 to 12 min, the RTK positioning results showed that the root-mean-square position error (RMSE) decreased by up to 95.13%, with an average of 65.31%, and that the percentage of epochs that passed the ratio test, which is the most common method for validating double differenced carrier phase integer ambiguity resolution, increased by up to 130%, with an average of 23.54%.