Guidelines recommend that primary care clinicians address a broad range of wellness topics, but time constraints limit clinicians’ ability to address them in the context of well child visits. A greater understanding of the salience of different wellness topics to families and clinicians may aid in prioritizing topics for practice-based interventions to promote wellness. We aimed to identify and compare parent and primary care clinicians’ priorities for early childhood wellness. We conducted a cross-sectional discrete choice experiment with 100 parents/guardians of 2–4-year old children and 27 clinicians from three pediatric primary care practices (two urban, one suburban). Participants rated the relative importance of 24 wellness attributes from six domains: child physical, mental, social, and educational health, family wellness, and community wellness. We compared the rankings of attributes across the parent and clinician samples to understand the differential priorities of the groups and examined the domains of attributes that were highly ranked. In both parent and clinician samples, the highest ranked attributes related to the child or family while community-level attributes were ranked lower. Parents and clinicians both highly prioritized the parent/child relationship and avoiding family substance use. Parents more strongly prioritized child learning while clinicians more strongly prioritized food security and parent mood. Neighborhood social cohesion and parent health problems were of low priority to both groups. Priorities were similar across subgroups of parent race, education, income, and neighborhood poverty. Findings may aid primary care practices and clinicians in prioritizing topics for interventions to promote wellness in pediatric primary care.