Background: Juvenile idiopathic arthritis-associated uveitis (JIA-U) is a rare condition, and assessment of the efficacy of disease-modifying antirheumatic drugs, synthetic (sDMARD) or biological (bDMARD), in randomized trials is hindered by this fact. Methods: In this prospective longitudinal study, we observed 38 children aged 1.3 to 15.2 years, with 69 eyes affected with JIA-U for 1970 overall eye examinations (6–59, median 16) irregularly scattered across 4.4–87.6 months (median 21.6) of follow-up, with on- and off-periods of DMARD use and use of topical treatments. Results: With adjustment for several time-invariant and time-varying covariates, periods of exposure to sDMARD vs. no DMARD exposure were associated with peak benefits of 15–20% lower probability of having more severe anterior chamber (AC) inflammation and a similar relative reduction in the daily use of topical corticosteroids (TCS). Periods of bDMARD exposure or of bDMARD + sDMARD exposure vs. no DMARD use were associated with peak benefits of an around 50% reduction in the probability of having more severe AC inflammation, and peak benefits of an around 60–65% reduction in TCS use. Conclusions: The observations regarding bDMARD (only) or bDMARD + sDMARD exposure are in agreement with the extent of benefits suggested for adalimumab vs. placebo (+background sDMARD) in the only existing randomized trial in this setting evaluating AC inflammation and TCS use.