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Background Nonlinear career paths are increasingly common. Women in academia pursuing nonlinear career paths experience negative impacts on career trajectory. No published studies have examined how pursuit of nonlinear career paths might perpetuate gender inequities within academic hospital medicine. Objective (1) Compare the frequency of nonlinear career paths by gender among academic hospitalists; (2) assess the perceived impact of two types of nonlinear career paths—extended leave (EL) and non-traditional work arrangements (NTWA) on hospitalists’ personal lives and careers. Design, Setting, and Participants Cross-sectional descriptive survey study of adult hospitalist physicians in three academic centers within the USA. Intervention Electronic survey including closed- and open-ended items assessing respondent utilization of and experiences with nonlinear career paths. Main Outcomes and Measures (1) Associations between EL and demographic variables as well as gender differences in leave length and NTWA strategies using Fisher’s exact test; 2) grounded theory qualitative analysis of open-text responses. Key Results Compared with men, women reported taking EL more often (p = 0.035) and for longer periods (p = 0.002). Men and women reported taking NTWA at similar rates. Women reported negative impacts of EL within domains of personal life, career, well-being, and work-life integration whereas men only reported negative impacts to career. Men and women described positive impacts of NTWA across all domains. Conclusions Women academic hospitalists reported taking EL more often than men and experienced disproportionately more adverse impacts to personal lives and careers. Surprisingly, men reported taking NTWA to address burnout and childbirth at similar rates to women. Our findings lay the groundwork for additional exploration of cultural and policy interventions, particularly improved paid leave policies. Supplementary Information The online version contains supplementary material available at 10.1007/s11606-022-07402-x.