Background Remote monitoring of pain using multidimensional mobile health (mHealth) assessment tools is increasingly being adopted in research and care. This assessment method is valuable because it is challenging to capture pain histories, particularly in children and young people in diseases where pain patterns can be complex, such as juvenile idiopathic arthritis (JIA). With the growth of mHealth measures and more frequent assessment, it is important to explore patient preferences for the timing and frequency of administration of such tools and consider whether certain administrative patterns can directly impact on children’s pain experiences. Objective This study aimed to explore the feasibility and influence (in terms of objective and subjective measurement reactivity) of several time sampling strategies in remote multidimensional pain reporting. Methods An N-of-1 trial was conducted in a subset of children and young people with JIA and their parents recruited to a UK cohort study. Children were allocated to 1 of 4 groups. Each group followed a different schedule of completion of MPT for 8 consecutive weeks. Each schedule included 2 blocks, each comprising 4 different randomized time sampling strategies, with each strategy occurring once within each 4-week block. Children completed MPT according to time sampling strategies: once-a-day, twice-a-day, once-a-week, and as-and-when pain was experienced. Adherence to each strategy was calculated. Participants completed the Patient-Reported Outcomes Measurement Information System Pain Interference Scale at the end of each week to explore objective reactivity. Differences in pain interference scores between time sampling strategies were assessed graphically and using Friedman tests. Children and young people and their parents took part in a semistructured interview about their preferences for different time sampling strategies and to explore subjective reactivity. Results A total of 14 children and young people (aged 7-16 years) and their parents participated. Adherence to pain reporting was higher in less intense time sampling strategies (once-a-week=63% [15/24]) compared with more intense time sampling strategies (twice-a-day=37.8% [127/336]). There were no statistically significant differences in pain interference scores between sampling strategies. Qualitative findings from interviews suggested that children preferred once-a-day (6/14, 43%) and as-and-when pain reporting (6/14, 43%). Creating routine was one of the most important factors for successful reporting, while still ensuring that comprehensive information about recent pain was captured. Conclusions Once-a-day pain reporting provides rich contextual information. Although patients were less adherent to this preferred sampling strategy, once-a-day reporting still provides more frequent assessment opportunities compared with other less intense or overburdensome schedules. Important issues for the design of studies and care incorporating momentary assessment techniques were identified. We demonstrate that patient reporting preferences are key to accommodate and are important where data capture quality is key. Our findings support frequent administration of such tools, using daily reporting methods where possible.