Diagnosing Borrelia miyamotoi disease (BMD) presents challenges due to its overlap with Lyme disease (LD) symptoms and the lack of reliable laboratory diagnostics. This case study demonstrates the successful use of phage-based PCR (phb-PCR) in identifying B. miyamotoi in a patient with multiple tick bites. A 46-year-old female presented with joint and muscle pain, chronic fatigue, and cognitive impairment after being bitten by ticks in Europe. Standard diagnostic tests, including Enzyme-linked immunosorbent assay (ELISA), immunoblot for LD, and antibody tests for Bartonella, Anaplasma, and autoimmune conditions, all returned negative results. However, phb-PCR identified the presence of B. miyamotoi. The patient was treated with intravenous ceftriaxone, oral azithromycin, and intravenous vitamin and mineral therapy, resulting in significant improvement in symptoms, including reduced pain, improved cognitive function, and decreased fatigue. This case emphasises the importance of direct diagnostic methods like phb-PCR for accurately identifying BMD, especially when conventional serological tests fail. Clinicians should consider testing for B. miyamotoi in cases of complex tick-borne diseases for timely and effective management.