Diagnostic accuracy was evaluated for various screening tools, including mobile health (mHealth) pure-tone screening, tympanometry, distortion product otoacoustic emissions (DPOAE), and inclusion of high frequencies to determine the most accurate screening protocol for identifying children with hearing loss in rural Alaska where the prevalence of middle ear disease is high. Hearing screening data were collected as part of two cluster randomized trials conducted in 15 communities in rural northwest Alaska. All children enrolled in school from preschool to 12th grade were eligible. Analysis was limited to data collected 2018 to 2019 (n = 1449), when both trials were running and measurement of high frequencies were included in the protocols. Analyses included estimates of diagnostic accuracy for each screening tool, as well as exploring performance by age and grade. Multiple imputation was used to assess diagnostic accuracy in younger children, where missing data were more prevalent due to requirements for conditioned responses. The audiometric reference standard included otoscopy, tympanometry, and high frequencies to ensure detection of infection-related and noise-induced hearing loss. Both the mHealth pure-tone screen and DPOAE screen performed better when tympanometry was added to the protocol (increase in sensitivity of 19.9%, 95% Confidence Interval (CI): 15.9 to 24.1 for mHealth screen, 17.9%, 95% CI: 14.0 to 21.8 for high-frequency mHealth screen, and 10.4%, 95% CI: 7.5 to 13.9 for DPOAE). The addition of 6 kHz to the mHealth pure-tone screen provided an 8.7 percentage point improvement in sensitivity (95% CI: 6.5 to 11.3). Completeness of data for both the reference standard and the mHealth screening tool differed substantially by age, due to difficulty with behavioral testing in young children. By age 7, children were able to complete behavioral testing, and data indicated that high-frequency mHealth pure-tone screen with tympanometry was the superior tool for children 7 years and older. For children 3 to 6 years of age, DPOAE plus tympanometry performed the best, both for complete data and multiply imputed data, which better approximates accuracy for children with missing data. This study directly evaluated pure-tone, DPOAE, and tympanometry tools as part of school hearing screening in rural Alaskan children (3 to 18+ years). Results from this study indicate that tympanometry is a key component in the hearing screening protocol, particularly in environments with higher prevalence of infection-related hearing loss. DPOAE is the preferred hearing screening tool when evaluating children younger than 7 years of age (below 2nd grade in the United States) due to the frequency of missing data with behavioral testing in this age group. For children 7 years and older, the addition of high frequencies to pure-tone screening increased the accuracy of screening, likely due to improved identification of hearing loss from noise exposure. The lack of a consistent reference standard in the literature makes comparing across studies challenging. In our study with a reference standard inclusive of otoscopy, tympanometry, and high frequencies, less than ideal sensitivities were found even for the most sensitive screening protocols, suggesting more investigation is necessary to ensure screening programs are appropriately identifying noise- and infection-related hearing loss in rural, low-resource settings.