The pandemic caused by COVID-19, although it is considered a threat to humanity, also changed the life of the entire planet in different aspects, one of them is education because in a short time it converted the classic face-to-face stage into a virtual stage, a product of compulsory confinement in almost every country in the world. In Peru, this change has many negative consequences, since teachers do not have or know of virtual technological tools to support the student in the learning process. To alleviate this problem, an augmented reality mobile application called ANATOMY-3D was developed, to help students learn and recognize the bones of bone system in 3D. The influence of ANATOMY-3D on the learning of students from a school in the Apurimac region, in Peru, was evaluated, for this, 53 students were taken as a sample, dividing them into an experimental group (GE1) and a control group (G2). the experimental group used ANATOMY-3D and the control group used the traditional method. The results were analyzed in three dimensions: usability, motivation, and a knowledge questionnaire. The results showed that ANATOMY-3D has a good level of usability, promotes better motivation in students to use ANATOMY-3D compared to the traditional method. Finally, the questionnaire showed that ANATOMY-3D positively influences the learning and recognition of the bones of bone system, as it achieved better scores for the experimental group (G1), compared to the control group (G2), with a difference of 0.88 in the mean of the grades.