Dr. Kratochvil is the Associate Vice Chancellor for Clinical Research at the University of Nebraska Medical Center (UNMC) and Vice President for Research for Nebraska Medicine, leading many of the clinical research initiatives for the academic health system. He is Executive Director of the Nebraska Global Center for Health Security. He serves as the Institutional Official for the UNMC Human Research Protection Program and Director of the UNMC Center for Clinical and Translational Research. Dr. Kratochvil is a Core Competency Advisor for Active and Passive Medical Defense against Weapons of Mass Destruction and Consequence Management for the National Strategic Research Institute. As the Medical Director of UNeHealth, which was formed to serve as a point of contact for commercial clinical research partnerships and growth, he oversees commercial contracting and agreements, facilitating clinical and translational research.

 Dr. Kratochvil served as Co-Principal Investigator of the federally-funded National Emerging Special Pathogens Training and Education Center (NETEC) which supports research and preparedness nationally for the management of special pathogens, and is a Co-Principal Investigator of the National Center for Health Security and Biopreparedness which train federal partners and provide quarantine services for the U.S.  He is a member of the Nebraska Biocontainment Unit leadership team, and member of the BioNebraska Board of Directors. His own research interests include clinical research and drug development, with a focus on highly pathogenic infectious diseases. 

Instrumental in the COVID-19 pandemic response initiated by Nebraska Medicine, activation of the Nebraska Quarantine unit, and the first approved COVID-19 research. In March 2020 he was appointed Chair of the Big Ten Task Force for Emerging Infectious Diseases.