The integration of phototherapy and optical waveguide technology is an innovative and promising approach to combat pathogens and tackle the rapidly emerging threat of multi-drug resistant microbes and viruses. Optical waveguides of which are ideally biodegradable, biocompatible, and mechanically compliant with the working environment can direct incident light to the immediate site of infection minimizing off-site effects and systemic side effects that are often inevitable with traditional phototherapy and pharmaceutical therapy, respectively. The use of optical waveguides for treatment of infection harnesses the benefits of phototherapy, meanwhile overcoming the barrier of limited penetration depth expanding the use of phototherapy to deep tissue infections. Through the multiple mechanisms of action that phototherapy provides and the precise delivery by optical waveguides, there is great potential to fulfill the requirements of infection control caused by a variety of pathogens including those refractories to conventional therapies while reducing the need for drug treatment.