Determining the content of the nutrient choline in foods and obtaining the required amount from the diet are crucial. One way to measure choline in foods is by converting choline esters to free choline via acid hydrolysis, followed by quantifying the total choline, as adopted by the AOAC method (AOAC-Choline); however, certain choline esters are difficult to hydrolyse. Here, we investigated various acid hydrolysis conditions to establish a reliable method for determining the total choline in foods by detecting free choline using highly sensitive and selective mass spectrometry. Hydrolysis in 0.055 mol/L HCl for 8 h in an autoclave (121 °C) was found to be optimal for the hydrolysis of choline esters in various foods. Twenty-four foods, including grains, seed, vegetables, fruits, mushroom, algae, fish, meats, beverage, processed foods, and egg, were measured. The trends in the total choline content were consistent with previous reports; however, the choline content was 10–20% higher than that measured using AOAC-Choline. Therefore, re-evaluation of the total choline content in foods using our constructed method is recommended. This reassessment will allow for a more reliable determination of choline intake for maintaining health.