This study aimed to compare the impact of different tools within the ImageJ program—specifically, the polygon and segmented line tools—on the calculation of muscle area and echo intensity (EI) values in ultrasound imaging of the vastus lateralis muscle. Thirteen volunteers participated, with ultrasound images acquired using 2D B-mode ultrasonography. The same evaluator used both tools to analyze the images, and reliability was assessed using the intraclass correlation coefficient (ICC) and coefficient of variation (CV). Bland–Altman plots were utilized to check agreement between measurements, and linear regression analysis was applied to evaluate proportional bias. The results showed that the reliability between the two tools for muscle area calculation was weak (r = 0.000; CV = 138.03 ± 0.34%), while it was excellent for EI measurements (r = 0.871; CV = 15.19 ± 2.96%). Bland–Altman plots revealed a large bias for muscle area (d = 195.2%) with significant proportional bias (p < 0.001). For EI, the bias was smaller (d = 15.2) but still significant (p = 0.028). A paired t-test confirmed significant differences between the two tools for muscle area (p < 0.001), though there was no significant difference for EI (p = 0.060). The findings suggest that the choice of tool in ImageJ significantly affects the measurement of muscle area, with the polygon tool yielding higher values, while EI measurements were relatively consistent between the two methods. This highlights the importance of tool selection in muscle analysis using ultrasound imaging.