Purpose: Papanicolaou (Pap) smear with assessment of cervical cytology may reduce the incidence and mortality rates of cervical cancer. However, poor quality Pap smears reduce screening efficacy. This study evaluated whether the "Teaching On The Run (TOTR)" teaching program could improve the skills of junior residents and enhance the quality of Pap smears. Methods: Between May and December 2015, 40 post-graduate year (PGY) residents were divided into two groups. The TOTR group (n = 22) participated in the protocol-driven TOTR teaching program, consisting of plan learning, learning, appraisal/assessment, feedback and outcome evaluation. The non-TOTR group (n = 18) participated in traditional large class learning. The rates of unidentifiable Pap smears and causes of unsatisfactory Pap smear were compared in the two groups. Results: The rates of unsatisfactory Pap smear quality (24.1% vs. 34.1%, p < 0.0001) and unidentifiable Pap smears (2.16% vs. 5.81%, p = 0.018) were significantly lower in the TOTR than in the non-TOTR group. TOTR training significantly reduced the numbers of scarce cells (8.2% vs. 12.8%, p < 0.005) and of overlapping cells or contained blood (3.6% vs. 5.8%, p < 0.005). Conclusions: The short-term TOTR training program effectively improves the skills of PGY residents in taking Pap smears, resulting in greater accuracy and Pap smear quality.