Prediction of RNA tertiary structure from sequence first relies on the prediction of secondary structure using free energy minimization. Hexaloops, hairpins with six nucleotides in the loop, are a common RNA secondary structure motif; however the current model used to predict their stability derived from data collected for hairpins of various sizes. Here, 19 hexaloops that are common in nature were optically melted to determine the thermodynamic parameters ΔH, ΔS, ΔGo37, and TM. By combining this data with 107 previously melted hexaloop sequences from the literature, a new hexaloop-specific model to predict free energy contribution was derived using a multivariable linear regression. Compared to the current model, this new model is more accurate and simpler to use. This updated model and new experimental data can be used in secondary structure prediction software to generate more accurate results.