The purpose of this study is to determine the use of evidence-based practice among doctors in specialty training at Instituto Nacional del Niño-San Borja in Lima, Peru. (INSN-San Borja). A total of 200 doctors in paediatric specialty training were included in this cross-sectional study. The Health Sciences Evidence-Based Practice (HS-EBP) questionnaire was performed to assess the use of evidence-based clinical practices. The questionnaire has five dimensions: “Beliefs and attitudes” (D1), “Results from scientific research” (D2), “Development of professional practice” (D3), “Assessment of results” (D4), and “Barriers and facilitators” (D5). Each of the five HS-EBP questionnaire dimensions had a median score of 107, 107, 79, 88, and 77, respectively. The ranges of possible scores in each dimension were as follows: from 12 to 120 in D1, D4, and D5; from 14 to 140 in D2; and from 10 to 100 in D3. This study shows that doctors in specialty training at the INSN-San Borja obtained median scores over the mean of possible scores in each of those dimensions, with a lower score in D5 (Barriers and facilitators). This shows that these doctors use evidence-based practice, however they consider there are barriers for its application. According to our observations, the main barrier is the lack of available time due to other clinical commitments.