High-precision Low Earth Orbit (LEO) satellite clocks are essential for LEO-augmented Positioning, Navigation, and Timing (PNT) services. Nowadays, high-precision LEO satellite clocks can be determined in real-time using a Kalman filter either onboard or on the ground, as long as the GNSS observations collected onboard LEO satellites can be transmitted to the ground in real-time. While various real-time and high-precision GNSS products are available nowadays in the latter case, their continuity and latencies in engineering reality are not as perfect as expected and will lead to unignorable impacts on the precision of the real-time LEO satellite clocks. In this study, based on real observations of Sentinel-3B, the impacts of different latencies and continuity of the real-time GNSS products on LEO real-time clocks are determined and discussed for two scenarios, namely the “epoch estimation” and “arc estimation” scenarios. The former case refers to the traditional filter-based processing epoch-by-epoch, and the latter case connects LEO satellite clocks from different rounds of filter-based processing under a certain arc length. The two scenarios lead to the “end-loss” and “mid-gap” situations. Latencies of the real-time GNSS products are discussed for the cases of orbit-only latency, clock-only latency, and combined forms, and different handling methods for the missing GNSS satellite clocks are discussed and compared. Results show that the real-time LEO satellite clock precision is very sensitive to the precision of real-time GNSS satellite clocks, and prediction of the latter becomes essential in case of their latencies. For the “end-loss” situation, with a latency of 30 to 120 s for the GNSS real-time clocks, the LEO satellite clock precision is reduced from about 0.2 to 0.28–0.57 ns. Waiting for the GNSS products in case of their short latencies and predicting the LEO satellite clocks instead could be a better option. For “arc-estimation”, when the gap of GNSS real-time products increases from 5 to 60 min, the real-time LEO clock precision decreases from 0.26 to 0.32 ns.