Female physicians often report lower self-confidence in their procedural and clinical competency compared to male physicians. There is limited data regarding self-reported confidence of female versus male trainees and any relation to objective competency in central venous catheter insertion. To analyze differences between male and female trainees in self-confidence and skill-based outcomes in placing central venous catheters. Using data from a central venous catheter simulation training program at a large tertiary medical center, we performed linear regressions to analyze confidence difference pre- and post-training, number of restarts, and number of cannulation attempts while controlling for baseline demographic characteristics of the sample. PGY-1 physician residents in all residency specialties who insert central venous catheters in the clinical setting at a tertiary academic center with a sample size of 281 residents. Confidence difference pre- and post-training measured on a Likert scale 1-5, number of restarts (novel global assessment variable), and number of cannulation attempts during the competency evaluation. Female trainees had both lower pre-program confidence (1.35 versus 1.74 out of 5, p < 0.001) and lower post-program confidence (3.77 versus 4.12 out of 5, p = 0.0021) as compared to male trainees. There was no statistically significant difference in number of restarts (95% CI - 0.073 to 0.368, p = 0.185) or cannulation attempts (95% CI - 0.039 to 0.342, p = 0.117) between sexes in linear regressions controlled for age, specialty designation, prior central venous catheter training, prior ultrasound guided vessel cannulation training, and pre-training confidence level. Female trainees rated their confidence significantly lower than their male counterparts both before and after the training program, despite no significant difference in skill-based outcomes. We discuss potential implications for trainees acquiring procedural skills during residency and for physician educators as they design training programs and delegate procedural opportunities.