Background Delayed-onset muscle soreness (DOMS) is a common condition in athletes characterized by muscle pain and stiffness after intense or unfamiliar exercise. It significantly impairs an athlete's performance by reducing muscle strength, flexibility, and overall physical capacity, often leading to suboptimal training or competition outcomes. Managing and mitigating DOMS is crucial for athletes to maintain peak performance and prevent potential injuries. The evaluation of effective treatment techniques is essential for expediting DOMS recovery by identifying biomarkers of skeletal muscle damage. This approach not only aids in optimizing recovery strategies but also contributes to the rehabilitation process, enabling athletes to return to peak performance quickly and safely. This study aims to evaluate the effects of shock wave therapy and diclofenac phonophoresis on serum creatine kinase levels in novice athletes suffering from DOMS in comparison to a control group. This research aims to assess the potential benefits of these therapeutic interventions in reducing skeletal muscle damage and enhancing recovery for individuals new to athletic training. Methodology A total of 48 novice athletes were recruited using simple random sampling and the block randomization approach to participate in this single-blind, multi-group, repeated-measures design. Male novice athletes in the age group of 18-25 years were included, and athletes with elevated serum creatine kinase variables at baseline measurements were excluded from the study. Before obtaining a written informed consent form, athletes were made aware of the procedure and associated risks. Group A received focused shock wave therapy, Group B received diclofenac phonophoresis, while Group C received no treatment. The Epley formula was used to compute the one-repetition maximum for each subject. Blood samples were taken at the baseline, 24, 48, 72, and 96 hours. Blood samples were taken before initiation of the study, as well as 24 hours, 48 hours, 72 hours, and 96 hours after DOMS was induced. Creatine kinase skeletal muscle biomarker was used as a dependent variable. Results In the evaluation of serum creatine kinase levels using analysis of variance (ANOVA), no statistically significant differences were observed between the three groups at baseline and 24-hour measurements (p > 0.05). However, statistically significant differences were found between the three groups at 48 hours, 72 hours, and 96 hours (p < 0.05). The repeated-measures ANOVA revealed significant overall changes in creatine kinase levels within the three groups, indicating time-dependent effects (p < 0.05). Specifically, during the 48 to 96-hour interval, the shock wave therapy group showed a lower mean value compared to the diclofenac phonophoresis group, followed by the control group. Conclusions The study demonstrates that a single administration of focused shock wave therapy effectively mitigated the elevation of creatine kinase levels in novice athletes with DOMS, surpassing the outcomes of diclofenac phonophoresis and the control group. These findings suggest the potential benefits of shock wave therapy in accelerating recovery from DOMS in the athletic population.