Oxygen consumption after exercise is frequently plotted as a function of time and then the area under the curve (AUC) is calculated. Subsequently, this AUC is further manipulated and thus, differences between these manipulations may impact the interpretation of changes in oxygen consumption after exercise. The purpose of this study was to determine if the method of calculating AUC influences the interpretation of changes in post-exercise oxygen consumption in response to long-term aerobic exercise. Forty-three moderately obese, sedentary participants volunteered to participate in this study (26 women and 17 men). All participants performed verified supervised exercise during the study. Supervised treadmill exercise was initially conducted for 3 d/week at 60% of heart rate reserve (HRR) for 30 min and progressed to 5 d/week at 75% of HRR for 45 min across the first 4 months. Pre-exercise, exercise, and post-exercise oxygen consumption was measured at baseline and 9 months. AUC was calculated by three methods; total, incremental, and positive incremental. Descriptive statistics and dependent T-tests were calculated for each method of calculating the AUC. In addition, the intra-individual coefficient of variation was determined for each individual for each AUC method. A pearson product moment correlation was calculated for each method to determine the strength of the relationship between pre- and post-training values. The change in post-exercise oxygen AUC after nine months of training was 5.36 ± 10.90 L, 2.17 ± 7.61 L, and 1.74 ± 9.10 L for the total, incremental, and positive incremental methods, respectively. There was significant change in post-exercise total AUC from baseline to 9-months (5.36 ± 10.90 L), while there was no significant change in incremental or positive incremental AUC. There was a moderately high correlation (r = 0.67, p < 0.05) between baseline and 9-months for the total AUC method, while there was no significant correlation for incremental and positive incremental AUC methods. These results suggest that the method used to calculate AUC can lead to a different interpretation of the effects of training on post-exercise oxygen consumption. From this data, it appears that analyzing post exercise oxygen consumption with the total area under the curve method has a greater ability to detect a change from aerobic training, than either the positive or incremental area under the curve methods.