Antimicrobial resistance (AMR) is a major threat to global human health. Improved AMR surveillance is one of six priorities identified by the World Health Organization to mitigate the burden of antibiotic-resistant infections. However, existing AMR genes do not explain all antibiotic-resistant infections. One common example is the Group A Streptococcus (GAS) infections that fail β-lactam (e.g. penicillin) therapy, despite universal susceptibility of this pathogen in vitro. Here we show that GAS strains isolated from penicillin treatment failures are able to invade into epithelial cells and replicate in the presence of penicillin, forming large intracellular bacterial communities. We further show that this process requires a GAS surface protein that promotes uptake into epithelial cells via an alternative invasion pathway, distinct from that used by most GAS strains. Our study describes a mechanism for phenotypic antibiotic resistance conferred by a bacterial invasin, and explains why penicillin often fails to clear GAS infections despite this pathogen being highly-susceptible to penicillin in vitro. Our findings may allow identification of GAS infections at risk of failing penicillin therapy at the point of care, and allow treatment with alternative antibiotics to reduce rates of recurrent GAS infections.