The delayed rectifier, IKr, is formed by homo/heterotetramers of the 2 HERG splice variants HERG1a and HERG1b. The only difference between isoforms is that HERG1b has a shorter N-terminal than HERG1a. Despite their similarities, HERG1a and 1b have profoundly different gating kinetics: HERG1b has faster activation and deactivation kinetics than HERG1a. HERG activation is a complex multi-step process involving voltage-dependent and voltage independent transitions.We used an envelope of tails protocol to isolate activation from the fast overlapping inactivation for both HERG1a and 1b. The activation rate of both HERG1a and 1b reaches an identical saturation value at very positive potentials, which suggests that the voltage-independent step is rate limiting at these potentials for both isoforms. This suggests that the voltage-insensitive step is not affected by isoform, i.e., the presence or absence of the N-terminal. At lower potentials, activation was strongly voltage dependent and was significantly different between isoforms. This indicates that the N-terminal modifies at least one voltage-sensitive step in the activation pathway. Deactivation is also strongly affected by the presence or absence of the N-terminal. This suggests that the N-terminal affects voltage-dependent transitions near the open state. Sensitivity analysis of our HERG model suggests that the effects may be more broad. Manipulation of only the early states failed to optimize the rate of deactivation, but optimization of only the final voltage dependent steps fails to recapitulate the combination of shifted steady-state activation and slope factor for the HERG1b isoform. In conclusion, our data indicate that the N-terminal interacts primarily through modification of voltage-sensitive transitions.