Antibiotics are an important part of medical practice for the treatment of bacterial infections. Antibiotic resistance has become one of the world's most critical public health threats. Clinical trials are used to compare strategies of antibiotic therapy for the treatment of bacterial infections. Antibiotic trials involve many scientific and practical challenges that need to be considered during trial design, conduct, and analysis. We review some of these challenges, discuss innovative approaches, and provide recommendations for addressing them to better inform practical medical decision‐making.