In response to recent regulatory guidelines, including ICH (International Council for Harmonisation) Q2 (R2) and Q14, we developed a UPLC-ELSD method to quantify Medium-Chain Triglycerides (MCTs) in Labrafac™ WL 1349 for nanoemulsion applications. This procedure, crafted using Analytical Quality by Design (AQbD) principles, addresses not only the validation of the methodology but also the lifecycle management challenges associated with the analysis of lipid-based excipients. Key parameters such as mobile phase composition, organic modifier, column type, flow rate, diluent, and column temperature were optimized to meet regulatory standards and ensure robustness in MCT quantification. Optimal conditions were achieved with a Waters Acquity HSS T3 (100 × 2.1 mm i.d., 1.8 μm) column at 33 °C, using a mixture of methanol (97.5%) and water (2.5%) containing 0.4% of formic acid at a flow rate of 0.41 mL/min. The method demonstrated an excellent fit on a cubic modelization for MCTs over a broad range of concentrations. Forced degradation studies, including hydrolytic (acidic and basic), oxidative, and thermal stress, confirmed the method’s suitability for possible stability scenarios. This validated UPLC method was successfully applied to quantitative analyses of bulk and formulation prototype samples containing MCTs. This AQbD-driven method enhances not only knowledge but also regulatory-compliant and cost-effective excipient control.