Aim: To compare systematically the impact of two novel insulin-dosing algorithms (the Pankowska Equation and the Food Insulin Index) with carbohydrate counting on postprandial glucose excursions following a high fat and a high protein meal. Methods: A randomized, crossover trial at two Paediatric Diabetes centres was conducted. On each day, participants consumed a high protein or high fat meal with similar carbohydrate amounts. Insulin was delivered according to carbohydrate counting, the Pankowska Equation or the Food Insulin Index. Subjects fasted for 5 h following the test meal and physical activity was standardized. Postprandial glycaemia was measured for 300 min using continuous glucose monitoring. Results: 33 children participated in the study. When compared to carbohydrate counting, the Pankowska Equation resulted in lower glycaemic excursion for 90–240 min after the high protein meal (p < 0.05) and lower peak glycaemic excursion (p < 0.05). The risk of hypoglycaemia was significantly lower for carbohydrate counting and the Food Insulin Index compared to the Pankowska Equation (OR 0.76 carbohydrate counting vs. the Pankowska Equation and 0.81 the Food Insulin Index vs. the Pankowska Equation). There was no significant difference in glycaemic excursions when carbohydrate counting was compared to the Food Insulin Index. Conclusion: The Pankowska Equation resulted in reduced postprandial hyperglycaemia at the expense of an increase in hypoglycaemia. There were no significant differences when carbohydrate counting was compared to the Food Insulin Index. Further research is required to optimize prandial insulin dosing.