Abstract Introduction The Oral Minimal Model (OMM), a differential-equations based mathematical model of glucose-insulin dynamics, utilizes data from a frequently sampled oral glucose tolerance test (OGTT) to quantify insulin sensitivity (S I). OMM-based estimates of S I can detect differences in insulin resistance (IR) across population groups and quantify effects of clinical or behavioral interventions. These estimates of S I have been validated in healthy adults using data from OGTTs with durations from 2 to 7 h. However, data demonstrating how protocol duration affects S I estimates in highly IR populations such as adolescents with obesity are limited. Methods A 6-h frequently sampled OGTT was performed in adolescent females with obesity. Two, 3-, and 4-hour implementations of OMM assuming an exponentially-decaying rate of glucose appearance beyond measured glucose concentrations were compared to the 6-h implementation. A 4-hour OMM implementation with truncated data (4h Tr) was also considered. Results Data from 68 participants were included (age 15.8±1.2 years, BMI 35.4±5.6 kg/m 2). Although S I values were highly correlated for all implementations, they varied with protocol duration (2h: 2.86±3.31, 3h: 2.55±2.62, 4h: 2.81±2.59, 4h tr: 3.13±3.14, 6h: 3.06±2.85 x 10-4 dl/kg/min per U/ml). S I estimates based on 2 or 3 h of data underestimated S I values, whereas 4-h S I estimates more closely approximated 6-h S I values. Discussion These results suggest that OGTT protocol duration should be considered when implementing OMM to estimate S I in adolescents with obesity and other IR populations.