Charlotte and Herbert S. Wagner, III established the Wagner Foundation in 2005. Initially, grants focused on elementary and secondary school programs, universities, hospitals, and human service organizations based in the Boston area. This local focus reflected an understanding of the community, a concern for accountability, and a desire to facilitate participation around shared goals.

Over time, the Wagner Foundation has expanded its community-focused methodology nationally and internationally. At the same time, the Wagner Foundation has expanded its mission to address issues of social justice that affect vulnerable communities in the United States and abroad. 

Internationally, they prioritize access to health care among the poorest communities and emphasize learning and economic development for women and children. Domestically, they focus on youth development, especially in job creation and learning, along with organizations that catalyze creative thinking and challenge convention.