Equine antimicrobial therapy has advanced over time with the availability of increasing pharmacokinetic and pharmacodynamic studies in horses, allowing for greater evidence‐based clinical decision‐making. However, many challenges to optimal antimicrobial therapy remain and further research is needed to address these areas. There are a limited number of approved antimicrobials for use in horses, which creates a need for compounded preparations for clinicians. Extra‐label drug use is commonplace in equine practice, which warrants continual education of veterinarians about policies and updates. Performance and competitive horses have their own unique concerns when it comes to antimicrobial use and drug testing. In keeping with the use of a broader range of antimicrobials over time, antimicrobial resistance is emerging as an important issue facing veterinary medicine, including equine practice. Another challenge is that of drug interactions and adverse drug events for which there are little scientific data available for horses, especially for critically important diseases such as Rhodococcus equi infection. Finally, much progress has been made in the availability of equine‐specific antimicrobial susceptibility break points. These aid clinicians in interpreting culture and susceptibility results and antimicrobial selection. Even with these advances, continuing education and further research are needed in this area.