This paper examines the management of secondary schools run by the Franciscan Sisters of St. Anna in Kenya. It begins with a brief history of the Congregation from its foundation in Oudenbosch to the time its mission began in Kenya. The guiding principle for Franciscan Sisters of St Anna schools is the Charism and sound traditions of the Congregation. The fostering of quality education and good administration of these schools have helped to inculcate good morals in the learners through Catholic teachings. Many of the schools were founded for the girl child, the vulnerable and the less fortunate in the society, thus echoing the mission of the Sisters; voice to the voiceless. The Sisters work hand-in-hand with Dutch and Kenyan governments to see the schools grow. The schools have a long-standing history of discipline and good morals. The paper highlights the sources of funds for the schools which include Government of Kenya, the Congregation through donors, and the parents. In the management of these schools, the principals see to it that there is; proper management of funds, professional development and motivation of staff for improved performance in learners. Finally, the paper discusses some challenges faced by the school administrators and how to overcome them.