Background and Objectives: Compared to other subjects, obese people have inferior trunk muscle endurance and balance. A modern method of neuro-muscular training called whole body vibration (WBV) may improve trunk muscle endurance and balance. This study evaluates the impact of a 4-week WBV program on trunk endurance and balance in obese female students. Materials and Methods: Sixty participants from 18 to 25 years of age and with BMI values ≥ 30 were randomly distributed into two equal groups: Group A (WBV group), who received 4 min of WBV, and Group B (sham WBV group), who received WBV with a turn-off device. The training was conducted two days/week for six weeks. Trunk endurance was evaluated using the Sorensen Test (ST) and Trunk Flexor Endurance Test (TFET). The Single-Leg Test (SLT) was used to assess static balance, while the Biodex Stability System measured dynamic balance. Results: The current study demonstrated no significant differences (p > 0.05) in pre-treatment variables between Groups A and B. Post-treatment, Group A showed a significantly higher duration of the Sorensen test, TFET and SLS than Group B (p < 0.001). Moreover, Group A showed significantly lower dynamic balance (p < 0.001) than Group B. Conclusions: WBV has a short-term effect on trunk endurance and balance in obese female students. WBV can be added to the rehabilitation program for obese subjects with deficits in trunk endurance and balance.