Background: Orthopedic implant-associated infections are difficult to eradicate because of biofilm formation and impaired healing. FK-16 and GF-17 are short synthetic antimicrobial fragments of the human cathelicidin LL-37; FK-16 consists of 16 amino acids and differs from the 17-amino-acid GF-17 by the absence of its N-terminal glycine. This study aimed to assess their acute tolerability following single-dose intravenous administration in mice and to evaluate the local antibacterial efficacy of FK-16 delivered via peptide-enriched silk fibroin (PSF) scaffolds in a rat model of methicillin-resistant Staphylococcus epidermidis (MRSE)-associated femoral nonunion. Methods: Thirty-six BALB/c mice (18 males and 18 females) received vehicle, FK-16, or GF-17 (0.1 or 1 mg/kg for each peptide) and underwent clinical and functional assessments, hemolysis testing, biochemical analyses, organ-weight measurements, and histopathological examination. Thirty-two male Wistar rats were assigned to a noninfected control group or infected groups treated with unloaded PSF, vancomycin-loaded PSF, or FK-16-loaded PSF. On day 56, antibacterial activity and bone healing were evaluated using microbiological culture, micro-computed tomography, and histopathology. Results: No mortality, persistent neurobehavioral abnormalities, or treatment-related organ lesions occurred in mice. Transient hind-limb paralysis occurred in one mouse treated with FK-16 and one treated with GF-17 at 1 mg/kg. Biochemical and hemolysis-related changes were isolated and did not follow a consistent dose–response pattern; no corresponding treatment-related organ lesions were observed. In rats, viable MRSE was recovered from 3/4 untreated specimens and none from those treated with vancomycin or FK-16. FK-16 was associated with partial normalization of the circulating ratio of osteoprotegerin to receptor activator of nuclear factor-κB ligand without significantly reducing early systemic inflammation. Bone mineral density, tissue mineral density, and bone volume fraction increased numerically, but no quantitative micro-computed tomography healing parameter improved significantly; the radiographic osteomyelitis score decreased significantly. Untreated PSF showed absent bridging, abundant fibrovascular tissue, chronic inflammation, rare Gram-positive cocci, and higher histological scores than noninfected controls; both treated groups showed minimal inflammation but incomplete bridging. Conclusions: FK-16 and GF-17 showed generally acceptable acute tolerability despite transient high-dose neurological effects. Locally delivered FK-16 demonstrated antibacterial activity, reduced osteomyelitis severity, and was associated with minimal histological evidence of inflammation, but did not significantly improve quantitative bone healing or restore complete bridging by day 56.