After completing her master's degree, Woody worked for a year as a faculty member and field supervisor in the division of nursing at Teachers College, Columbia University. She then returned to the South, where she served as the assistant director for medical and surgical nursing Emory University Hospital in Atlanta, Georgia between 1956 and 1968. During this time, Woody also worked as a co-instructor for the master's program in nursing supervision at the Nell Hodgson Woodruff School of Nursing. In 1968, Woody left Emory to accept the positions of assistant hospital director and director of nursing at Grady Memorial Hospital. She would continue to serve in these positions until 1979. While working at Grady, Woody helped create a diabetes day care program, specialized nurse-managed clinics, and a patient education program. She also established clinical specialist positions in pediatrics, psychiatry, surgical rehabilitation, and burns. Woody also recruited Elizabeth Sharp to found Grady's first nurse midwifery program. Throughout her time at Grady, Woody retained her role as an assistant professor of nursing at the Nell Hodgson Woodruff School of Nursing. In 1979, she became the founding dean at the Auburn University School of Nursing. Over the course of the five years she served in this position, Woody helped develop a practice oriented undergraduate nursing program. Woody returned to Emory University in 1984 to serve as both the director of nursing and the associate hospital director. During this period, she also served as the associate dean of the Nell Hodgson Woodruff School of Nursing. During this period at Emory, Woody helped to established a collaborative model that allowed hospital nurses to teach students and nursing faculty to maintain a clinical practice. She also created several new positions for nurses in transplantation medicine and pain and incontinence management. On September 15, 1992 Woody was named the interim dean of the nursing Nell Hodgson Woodruff School of Nursing. She held this position for one year. Woody retired from nursing on October 1, 1993, at the age of 67. Throughout her career, Woody advocated for the integration of professional associations in nursing. She led the integration of the American Nurses Association. She also served on numerous committees over the years. Most notably, she served as the chairperson and board of directors of the American Journal of Nursing Company. She also served as a charter fellow of the American Academy of Nursing and a member of the board of directors of Wesley Homes. Woody also held numerous professional memberships including the American Academy of Nursing, National League for Nursing, the American Nurses' Association. Woody published several articles and essays. Her works were often featured in the American Journal of Nursing. In 1973, Woody also a co-authored the book Applying the Problem-Oriented System with John Willis Hurst and Henry Kenneth Walker. Nursing students at Auburn University can be considered for the Mary F. Woody Alumni Endowed Scholarship.