According to self-determination theory, frustration of basic psychological needs (autonomy, competence, and relatedness) leads to ill-being and negatively affects the learning process. The present study aimed to analyze the effects of a gamified creativity-based teaching method of human anatomy on basic psychological needs frustration compared with a conventional teaching method. A quasi-experimental design was employed, comparing two anatomy educational treatments (experimental and control) over a 7-week period. A total of 116 first-year students from two Spanish public universities was participated. The Basic Psychological Needs Frustration Scale was utilized, and pre- and post-treatment measurements were collected. Statistical analyses included independent samples t-tests, one-way ANCOVAs, and a factorial repeated measures ANCOVA 2 × 2 (time × treatment), comparing two groups based on time (baseline vs. follow-up) and treatment (control vs. experimental). The analysis revealed that the gamified creativity-based program achieved lower frustration of basic psychological needs compared to the control treatment (t (108) = 3.74, p < 0.001, d = 0.68) and a treatment effect was observed (F (1) = 9.06, p = 0.003, [partial eta-squared] = 0.083). Autonomy and competence frustration significantly increased in the control group, while apparently remained consistent over time in the treatment group. Baseline and follow-up significant differences were found for relatedness (t (114) = 1.12, p = 0.03, d = 0.4; t (110) = 2.88, p = 0.005, d = 0.53, respectively), as well as a treatment effect (F (1) = 7.28, p = 0.008, [partial eta-squared] = 0.069). These findings provide support for the idea that students' basic psychological needs are lower frustrated with the implementation of a gamified creativity-based teaching method in anatomy education.