The advancement of educational technology has allowed the development of new forms of learning in digital environments such as flipped learning and augmented reality, making possible the implementation of innovative experiences in the school environment, such as the intervention displayed in this manuscript concerning the learning of the BLS and CPR protocols. The objective of the study is to know the type of methodology (traditional or innovative) most effective for learning a health education program. For this, an experimental design with a control group and a single posttest measurement was used. A sample of 60 Spanish students from the third year of Compulsory Secondary Education was taken to display an experimental design of the control (n = 30) and experimental group (n = 30). The data were collected through a questionnaire validated by Delphi method and of relevant reliability (α = .860). The results reveal a greater progress of the experimental group, following a methodology with flipped learning and augmented reality, with respect to the control group of traditional learning, assuming improvements in motivation, participation, interaction, flexibility, autonomy and, consequently, an effective achievement of the didactic objectives. Therefore, it is concluded that the innovative methodology favors the acquisition and greater projection of the learning of the protocol guidelines about the BLS and CPR.