Background: Fibromyalgia is a chronic condition characterized by a complex array of symptoms that impact multiple domains, including physical, psychological, and social aspects of an individual’s well-being. Although home-based adapted physical activity (HAP) interventions represent a promising strategy to improve health-related physical fitness (PF), studies on the topic are still lacking and further research is required. The objective of the present study was to evaluate the impact of participation in a 12-week HAP intervention on health-related PF in adult women with fibromyalgia syndrome (FS). Methods: Participants were women with fibromyalgia (n = 29; 47.1 ± 9.5 yrs) assigned to the 12-week HAP program (n = 17) or wait-list control group (n = 12). Participants completed two weekly circuit-training sessions delivered through an online platform. PF components were assessed through a standardized test battery: 30-s chair stand (lower-body strength), arm curl (upper-body strength), 2-min step (cardiorespiratory fitness), back scratch (flexibility) and 8-foot up-and-go test (agility and balance). Three time-point evaluations were planned: at baseline (T0), after 6 weeks (T1), and after 12 weeks (T2). Linear mixed models were used, and partial eta-squared (η²p) effect sizes were calculated. Results: A significant time × group interaction emerged for upper body strength (p = 0.001; η²p = 0.404), agility (p < 0.001; η²p = 0.569) and cardiorespiratory fitness (p = 0.009, η²p = 0.292). Specifically, from baseline to 12 weeks, the experimental group improved in the arm-curl test (from 15.8 ± 4.5 to 18.9 ± 5.0 repetitions), agility (from 6.6 ± 1.5 to 5.2 ± 1.1 s), and cardiorespiratory fitness (from 69.1 ± 18.8 to 77.2 ± 21.1 repetitions), while the control group showed no meaningful changes. Conclusions: The participation in a 12-week HAP intervention had a positive impact on different components of PF in women with FS, which may have implications for greater physical autonomy and well-being.