Recovery and reuse of high-acidity vegetable oil waste (higher content of free fatty acids) is a major concern for reducing their effect on the environment. Moreover, the conventional deacidification processes are known to show drawbacks, such as oil losses or higher costs of wastewater treatment, for which it requires great attention, especially at the industrial scale. This work presents the design of a highly efficient and sustainable process for Camelina sativa oil deacidification by using an ecofriendly method, namely molecular distillation. Experimental studies were performed to identify operating conditions for removing of free fatty acids (FFA) by molecular distillation which involves the oil evaporation in high vacuum conditions. The experimental studies were supported by statistical analysis and technical-economic analysis. Response surface methodology (RSM) was employed to formulate and validate second-order models to predict deacidification efficiency, FFA concentration, and triacylglyceride (TAG) concentration in deodorized oil based on three parameters effects, validated by statistical p-value < 0.05. For a desirability function value of 0.9826, the optimal parameters of evaporator temperature at 173.5 °C, wiper speed at 350 rpm, and feed flowrate at 2 mL/min were selected. The results for process design at optimal conditions (using conventional and molecular distillation methods) showed an efficiency over 92%, a significant reduction in FFA (up to 1%), and an increase in TAG (up to 93%) in refined oil for both methods. From an economical point of view, the deacidification by molecular distillation of Camelina sativa oil is a sustainable process: no wastewater generation, no solvents and water consumption, and lower production costs, obtaining a valuable by-product (FFA).