Academic global health collaborations have the potential to improve joint understanding of health issues in low- and middle-income countries (LMICs). Our objective was to elucidate perceptions of benefits and challenges of academic global health collaborations as well as areas for improving collaborative research conducted in LMICs. This cross-sectional, mixed-methods study surveyed investigators' perceptions of benefits and challenges of pediatric academic global health collaborations. Authors of articles from four pediatric journals reporting pediatric research conducted in LMICs published between 2006 and 2015 were surveyed. Responses of LMIC investigators were compared with those of investigators in high-income countries (HICs). Responses to open-ended questions were analyzed using a combined thematic and content analysis approach. Of 1,420 potential respondents, 252 (17.7%) responded to the survey. Collaborative research with investigators from other countries was perceived as beneficial by 88.5% of respondents (n = 223), although this perception was more common among HIC respondents (n = 110, 94.0%) than LMIC respondents (n = 113, 83.7%) (p = 0.014). Sixty-seven percent (n = 170) of respondents perceived that HIC investigators had set the research agenda in work conducted in a LMIC. Respondents identified several critical factors to improve academic global health collaborations, including research capacity building, communication, and early involvement of LMIC investigators with shared decision-making during study conception and grant writing. Pediatric academic global health collaboration was widely perceived as positive. However, despite calls for capacity building and locally generated research ideas, many respondents felt that HIC investigators set the research agenda for work conducted in LMICs. This study provides suggestions for improving collaboration among pediatric academicians globally.