Streptococcal bacteremia that occurs during invasive dental procedures can lead to infective endocarditis (IE) in children with certain heart diseases. Prior to such procedures, antibiotic prophylaxis (AP) with amoxicillin (AMPC) is recommended. However, the detection of amoxicillin-resistant strains (AMPC-RS) in the mouths of children with heart diseases raises the concern that they would be uncovered by the action of standard AP. This work carried out a systematic review and meta-analysis regarding AMPC-RS carriage in the mouths of children. We consulted databases covering studies between the years 2000 and 2021, following the PRISMA declaration. A meta-analysis was carried out to assess the prevalence of children carrying AMPC-RS in the mouths. The antimicrobial tests were carried out by microdilution (46.2% of articles), disk diffusion (38.3%), and the E-test (15.4%). Streptococcus mitis and S. sanguinis were bacteria with the most found resistance phenotype, with MIC reaching values of 128 µg/mL. Of the 13 selected articles, only 6 presented results that made it possible to calculate the prevalence of children carrying AMPC-RS in their mouths, ranging from 5.5% to 86.3%. Most of the studies were classified as high quality, and the collected data demonstrate the presence of streptococcal strains with different levels of resistance in the collected samples, such as the dental plaque. The meta-analysis pointed to evidence of AMPC-RS being carried, with a prevalence of 21.3% (I² = 0%, p = 0.705). There is an important prevalence of AMPC-RS carriage in the mouths of children. Specific attention should be directed to AP in those susceptible to IE.