Background Typing on smartphones, which has become a near daily activity, requires both upper limb and cognitive function. Analysis of keyboard interactions during regular typing, that is, keystroke dynamics, could therefore potentially be utilized for passive and continuous monitoring of function in patients with multiple sclerosis. Objective To determine whether passively acquired smartphone keystroke dynamics correspond to multiple sclerosis outcomes, we investigated the association between keystroke dynamics and clinical outcomes (upper limb and cognitive function). This association was investigated longitudinally in order to study within-patient changes independently of between-patient differences. Methods During a 1-year follow-up, arm function and information processing speed were assessed every 3 months in 102 patients with multiple sclerosis with the Nine-Hole Peg Test and Symbol Digit Modalities Test, respectively. Keystroke-dynamics data were continuously obtained from regular typing on the participants’ own smartphones. Press-and-release latency of the alphanumeric keys constituted the fine motor score cluster, while latency of the punctuation and backspace keys constituted the cognition score cluster. The association over time between keystroke clusters and the corresponding clinical outcomes was assessed with linear mixed models with subjects as random intercepts. By centering around the mean and calculating deviation scores within subjects, between-subject and within-subject effects were distinguished. Results Mean (SD) scores for the fine motor score cluster and cognition score cluster were 0.43 (0.16) and 0.94 (0.41) seconds, respectively. The fine motor score cluster was significantly associated with the Nine-Hole Peg Test: between-subject β was 15.9 (95% CI 12.2-19.6) and within-subject β was 6.9 (95% CI 2.0-11.9). The cognition score cluster was significantly associated with the Symbol Digit Modalities Test between subjects (between-subject β –11.2, 95% CI –17.3 to –5.2) but not within subjects (within-subject β –0.4, 95% CI –5.6 to 4.9). Conclusions Smartphone keystroke dynamics were longitudinally associated with multiple sclerosis outcomes. Worse arm function corresponded with longer latency in typing both across and within patients. Worse processing speed corresponded with higher latency in using punctuation and backspace keys across subjects. Hence, keystroke dynamics are a potential digital biomarker for remote monitoring and predicting clinical outcomes in patients with multiple sclerosis. Trial Registration Netherlands Trial Register NTR7268; https://trialsearch.who.int/Trial2.aspx?TrialID=NTR7268