Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disease. Its slow and variable progression makes the development of new treatments highly dependent on validated biomarkers that can quantify disease progression and response to drug interventions. We aimed to build a tool that estimates FSHD clinical severity based on behavioral features captured using smartphone and remote sensor data. The adoption of remote monitoring tools, such as smartphones and wearables, would provide a novel opportunity for continuous, passive, and objective monitoring of FSHD symptom severity outside the clinic. In total, 38 genetically confirmed patients with FSHD were enrolled. The FSHD Clinical Score and the Timed Up and Go (TUG) test were used to assess FSHD symptom severity at days 0 and 42. Remote sensor data were collected using an Android smartphone, Withings Steel HR+, Body+, and BPM Connect+ for 6 continuous weeks. We created 2 single-task regression models that estimated the FSHD Clinical Score and TUG separately. Further, we built 1 multitask regression model that estimated the 2 clinical assessments simultaneously. Further, we assessed how an increasingly incremental time window affected the model performance. To do so, we trained the models on an incrementally increasing time window (from day 1 until day 14) and evaluated the predictions of the clinical severity on the remaining 4 weeks of data. The single-task regression models achieved an R2 of 0.57 and 0.59 and a root-mean-square error (RMSE) of 2.09 and 1.66 when estimating FSHD Clinical Score and TUG, respectively. Time spent at a health-related location (such as a gym or hospital) and call duration were features that were predictive of both clinical assessments. The multitask model achieved an R2 of 0.66 and 0.81 and an RMSE of 1.97 and 1.61 for the FSHD Clinical Score and TUG, respectively, and therefore outperformed the single-task models in estimating clinical severity. The 3 most important features selected by the multitask model were light sleep duration, total steps per day, and mean steps per minute. Using an increasing time window (starting from day 1 to day 14) for the FSHD Clinical Score, TUG, and multitask estimation yielded an average R2 of 0.65, 0.79, and 0.76 and an average RMSE of 3.37, 2.05, and 4.37, respectively. We demonstrated that smartphone and remote sensor data could be used to estimate FSHD clinical severity and therefore complement the assessment of FSHD outside the clinic. In addition, our results illustrated that training the models on the first week of data allows for consistent and stable prediction of FSHD symptom severity. Longitudinal follow-up studies should be conducted to further validate the reliability and validity of the multitask model as a tool to monitor disease progression over a longer period. ClinicalTrials.gov NCT04999735; https://www.clinicaltrials.gov/ct2/show/NCT04999735.