System latency (i.e., time between user action and system response) has known detrimental effects, particularly in the increasingly prevalent complex human–computer interaction types (e.g., higher control order like in games or teleoperation). The objective of the present research was to examine the impact of low-range latencies on behaviour (performance, control) and perception (perceived control difficulty, latency) in an unstable system with second-order control. Furthermore, the influence of the controller gain (affecting the system’s sensitivity to user input) on latency effects was investigated. The study extends existing research through examining multiple parameters of human–computer interaction in relation to differing levels of low-range latencies (14–198 ms). For this aim, participants across two experiments performed a second-order control task consisting of balancing a ball on a beam using a low-latency computer system with varying levels of added latency. Latency affected performance even with the smallest added latency of 14 ms (d = 0.61). A larger controller gain increased latency effects on control indicators (all d ≥ 0.68) and perceived control difficulty (d = 0.85). Latency impacted performance, control parameters and perceived control difficulty prior to participants’ awareness of the latency. Thus, optimizing latency can be important regardless of whether the user perceives the latency. The diverse effects regarding the different parameters emphasize the usefulness of a comprehensive latency effect assessment and indicate human adaptation to latency.