Silk fibroin (SF) and sodium alginate (SA) are natural polymers with interesting properties to produce biomaterials. Blends of these polymers form a complex protein–polysaccharide system where phase separation can be observed. Therefore, the thermodynamic analysis of this system is important to understand the interaction between the polymers and predict the final state and composition of the phases found in these blends. This study explored blends with a different initial composition of SF, SA, and water at 25°C and neutral pH. The influence of the proportion between mannuronic and guluronic acids on SA composition was investigated. After phase separation, two phases were identified, and the equilibrium data were fitted on three different thermodynamic models: Flory–Huggins, non-random two-liquids, and universal quasichemical. Cohn equation was also used to investigate the potential of SA to precipitate the SF in solution. The results show that the proportion of mannuronic and guluronic acids on the SA can significantly influence on equilibrium data and on the SF/SA interaction parameter, hence, becoming a variability factor if this parameter is not under control in formulations.