AbstractPeople with methamphetamine use disorder (MUD) struggle to shift their behaviour from methamphetamine‐orientated habits to goal‐oriented choices. The model‐based/model‐free framework is well suited to understand this difficulty by unpacking the computational mechanisms that support experienced‐based (model‐free) and goal‐directed (model‐based) choices. We aimed to examine whether 1) participants with MUD differed from controls on behavioural proxies and/or computational mechanisms of model‐based/model‐free choices; 2) model‐based/model‐free decision‐making correlated with MUD symptoms; and 3) model‐based/model‐free deficits improved over six weeks in the group with MUD. Participants with MUD and controls with similar age, IQ and socioeconomic status completed the Two‐Step Task at treatment commencement (MUD n = 30, Controls n = 31) and six weeks later (MUD n = 23, Controls n = 26). We examined behavioural proxies of model‐based/model‐free decisions using mixed logistic regression, and their underlying mechanisms using computational modelling. At a behavioural level, participants with MUD were more likely to switch their choices following rewarded actions, although this pattern improved at follow up. At a computational level, groups were similar in their use of model‐based mechanisms, but participants with MUD were less likely to apply model‐free mechanisms and less likely to repeat rewarded actions. We did not find evidence that individual differences in model‐based or model‐free parameters were associated with greater severity of methamphetamine dependence, nor did we find that group differences in computational parameters changed between baseline and follow‐up assessment. Decision‐making challenges in people with MUD are likely related to difficulties in pursuing choices previously associated with positive outcomes.