Background: Fibromyalgia (FM) is a chronic syndrome characterized by widespread musculoskeletal pain, fatigue, sleep disturbances, and cognitive and affective symptoms. Objectives: This study aimed to examine the acute effects of Resistance Training (RT) and Pilates on pain, functional impact, flexibility, and health-related quality of life in individuals with FM. Methods: In this randomized crossover pilot study, eight adults (7 females, 1 male; mean age: 48.5 ± 8.2 years) with a clinical diagnosis of FM participated. Each participant performed both RT and Pilates sessions in a randomized order. Outcomes were assessed at baseline and 24 h post-intervention using the Fibromyalgia Impact Questionnaire (FIQ), the 36-Item Short Form Health Survey (SF-36), the Visual Analog Scale (VAS) for pain, and the Wells sit-and-reach test (WELLS). Data were analyzed using two-way repeated-measures ANOVA and paired t-tests, with effect sizes (η²p and Cohen’s d) and 95% confidence intervals (95% CI). Statistical significance was set at p < 0.05. No formal sample size calculation was performed. Results: Participants presented a mean body mass index (BMI) of 27.4 ± 4.1 kg/m² and time since diagnosis of 6.2 ± 3.1 years. Within-subject variations were observed following both interventions. FIQ scores decreased at 24 h after both RT and Pilates sessions (RT: 52.21 ± 18.61; Pilates: 45.50 ± 18.63; p = 0.038, η²p = 0.42, 95% CI [−12.5, −1.2]). Conclusions: Both Resistance Training and Pilates acutely reduced overall disease impact in individuals with fibromyalgia, with Pilates promoting superior acute gains in posterior chain flexibility.