Background and Objectives: Whole-body electromyostimulation is under investigation as a potential aid for obesity-related health problems, supplementing a comprehensive, evidence-based obesity management strategy that includes lifestyle, diet, and exercise. The study investigated the impact of a whole-body electromyostimulation training program on physical performance and cardiometabolic markers in young obese females. Materials and Methods: Twenty-eight obese females, aged over 18 years with BMI over 30 and body fat over 28% and no underlying health conditions or medication, were divided into a whole-body electromyostimulation group (15 participants) and a control group (13 participants). The whole-body electromyostimulation program lasted 12 weeks, with two 20 min sessions weekly, using bipolar, rectangular current. Assessments pre and post intervention included body composition, blood pressure, lipid profile, C-reactive protein levels, maximal oxygen consumption, and jumping and sprint performance. Two-way ANOVA and t-tests were used for analysis. Results: Statistical analysis revealed significant (group × time) interactions for body composition, systolic blood pressure, maximal oxygen consumption, jumping and sprint performance, and plasma levels of lipids and C-reactive protein. Post hoc analyses for the whole-body electromyostimulation group indicated improvements in body composition indices (p < 0.01), systolic blood pressure (p = 0.003), maximal oxygen consumption (p = 0.010), and both jumping and 30 m sprint performance (p < 0.001 and p = 0.001, respectively) after the intervention. Furthermore, plasma levels of lipids (p < 0.01) and C-reactive protein (p = 0.002) showed significant improvements following the training program. In contrast, no significant changes were observed for these variables in the control group. Conclusions: A 12-week whole-body electromyostimulation program significantly improved body composition (skeletal muscle mass, body mass index, body fat, and waist circumference), physical performance (maximal oxygen consumption, jumping and sprint performance), and certain cardiometabolic (plasma level of lipids) and inflammatory markers (C-reactive protein) in obese young women. Further research is needed to explore the broader effects of whole-body electromyostimulation on physical and cardiometabolic health.