BACKGROUND: Online surveys can align with youths increased use of the internet and can be a mechanism for expanding youth participation in research. This is particularly important during the coronavirus disease 2019 (COVID-19) pandemic, when in-person interactions are limited. However, the advantages and drawbacks of online systems used for research need to be carefully considered before utilizing such methodologies. AIM: To describe and discuss the strengths and limitations of an online system developed to recruit adolescent girls for a sexual health research study and conduct a three-month follow up survey. METHODS: This methodology paper examines the use of an online system to recruit and follow participants three months after their medical visit to evaluate a mobile sexual and reproductive health application, Health-E You/Salud iTuTM, for adolescent girls attending school-based health centers (SBHCs) across the United States. SBHC staff gave adolescent girls a web link to an online eligibility and consent survey. Participants were then asked to complete two online surveys (baseline and 3-month follow-up). Surveys, reminders, and incentives to complete them were distributed through short message service (SMS) text messages. Upon completing each survey, participants were also sent an email with a link to an electronic gift card as a thank-you for their participation. Barriers to implementing this system were discussed with clinicians and staff at each participating SBHC. RESULTS: This online recruitment and retention system enabled participant recruitment at 26 different SBHCs in seven states across the United States. Between September 2021 and June 2022, 415 adolescent girls were screened using the Qualtrics online survey platform, and 182 were eligible to participate. Of those eligible, 78.0% (n = 142) completed the baseline survey. Participants were racially, geographically, and linguistically diverse. Most of the participants (89.4%) were non-White, and 40.8% spoke Spanish. A total of 62.0% (n = 88) completed the 3-month follow-up survey. Limitations of this system included reliance on internet access (via Wi-Fi or cell service), which was not universally available or reliable. In addition, an individual unrelated to the study obtained the survey link, filled out multiple surveys, and received multiple gift cards before the research team discovered and stopped this activity. As a result, additional security protocols were instituted. CONCLUSION: Online systems for health research can increase the reach and diversity of study participants, reduce costs for research personnel time and travel, allow for continued study operation when in-person visits are limited (such as during the COVID-19 pandemic), and connect youth with research using technology. However, there are challenges and limitations to online systems, which include limited internet access, intermittent internet connection, data security concerns, and the potential for fraudulent users. These challenges should be considered prior to using online systems for research.