Proper management of logistical issues in Teacher education programme tends to promote the quality of preparation of school teachers. The main objective of the study was to investigate challenges of administering teacher education programmes in Kenyan universities. The theoretical framework of the study was adopted as used by Koehler and Mishra's concept of technological pedagogical content knowledge. The study was conducted in public and private universities in Kenya. Purposive, random and stratified sampling techniques were used to select the subjects for the study. The sample size comprised of 59 lecturers and 635 fourth-year students drawn from the selected universities. The research instruments included questionnaires and interview schedule. The study established that challenges in teacher education are real in nature and require urgent address. These challenges were broadly characterized as institutional-based (university) and extra institutional-based (outside the institution) in nature. These challenges result in preparation and production of poor quality of school teachers at university level in Kenya. It is therefore recommended that the identified challenges require collaborative action and decision-making by relevant stake-holders in teacher education programmes and Kenyan universities offering teacher preparation programmes. In order to confront the noted challenges there is need to develop and use innovative practices in teacher education.