Background <p>Effective teaching of veterinary anatomy is essential for developing diagnostic reasoning and practical competence. Traditional lecture-based approaches often promote rote memorization and limited engagement. Project-based learning (PBL) has been proposed as an active, student-centered alternative that fosters deeper understanding, teamwork, and skill development.</p> Methods <p>A descriptive mixed-methods study was conducted among first-year veterinary students (<i>n</i> = 76) at King Salman International University, Egypt, to assess perceptions, experiences, and challenges associated with PBL in veterinary anatomy. Data were collected through an anonymous online questionnaire combining Likert-scale and open-ended items. Quantitative data were analyzed using descriptive statistics, non-parametric tests, and Spearman’s correlations, while qualitative responses underwent thematic analysis.</p> Results <p>Most participants (96%) perceived PBL as valuable, and all (100%) agreed it enhanced understanding and retention of anatomical concepts. High motivation was reported by 63% of students, and 97.4% confirmed improvements in hands-on and technical skills. Team satisfaction correlated positively with clear task division (r = + 0.74) and instructor feedback (r = + 0.68). Smaller teams (≤ 4 members) showed higher engagement (<i>r</i> = − 0.42). Students highlighted enhanced motivation, creativity, and teamwork as major benefits. Key challenges included limited material quality, time constraints, and insufficient instructor support.</p> Conclusion <p>PBL proved to be an effective pedagogical strategy for veterinary anatomy, promoting deep learning, collaboration, and practical competence. Addressing logistical and instructional challenges, improving feedback mechanisms, and integrating digital tools may further optimize its implementation. Future research should compare PBL with traditional methods and evaluate long-term educational outcomes.</p>