Whaley Children's Center was founded by Robert H. Whaley, a successful businessman and generous philanthropist in Flint, Mich. Having been president of Citizens Bank for over 40 years, Robert and his wife Mary McFarlan Whaley had secured enough wealth to bequeath the funds to establish the Donald M. Whaley Memorial Home after his death in 1922. Forty years prior, Robert and Mary's son, Donald, passed away from diphtheria at the age of 10. While sorting through his possessions after his death, Robert and Mary found a jar of coins Donald had been saving to donate to the children less fortunate than himself living in a children's home in Detroit.

The Whaley Foundation was incorporated January 26, 1924 with a mission of providing care for "homeless and neglected children." The fund was left to the trusteeship of the wardens and vestry of St. Paul's Episcopal Church in Flint, Mich. Charles Stewart Mott and C.F. Barth, president and vice-president of the Board of Trustees, wanted the best and most modern type of children's home consistent with Robert's will. They consulted with the Child Welfare League of America who surveyed the needs of Flint and recommended, "The Whaley Fund equip itself with a place and staff to serve dependent and neglected children in general without distinction to race and creed and particularly to those cases that were in trouble because of health and behavior conditions that had not been diagnosed and remedied."

There have been a number of significant additions to Whaley facilities throughout the institution's 90+ years. In 1955, a recreational building with a gym, craft room and two classrooms was built on campus. In 1964, the children's living units underwent a major renovation for the first time since the building was built, and in 1969, the group home program begun. This program was expanded in the 1990s when, through the support and generosity of three local service clubs, Optimist, Rotary and Zonta, three group homes were established in nearby neighborhoods.

Whaley Children's Center has remained aware of the changing needs in the area of child welfare. In 1977, Whaley was one of the first agencies to offer a Treatment Foster Care Program providing children the opportunity to live with a specially trained family. During the same year Whaley opened the Educational Center attached to the Recreational Building including five classrooms, several offices and a meeting room. In 1982, a Special Needs Adoption program had begun.

In 1991, the C. S. and Ruth Rawlings Mott Residential Center was opened as a state of the art residential treatment center. In 1993, the Whaley Memorial Building was remodeled into a functional office building for clinical, foster care, adoption, administrative, human resource, finance and development offices.

Currently, Whaley Children's Center provides shelter, hope and healing to nearly 90 children each year who are survivors of horrific abuse and neglect. Through an intense treatment process provided by qualified and dedicated staff, children are taught the skills necessary to thrive in life as well as given strategies to cope with their past and press on to greater futures.