One of the major innovations of the Ford Foundation International Fellowships Program was a decentralized operational structure linking implementing organizations in the twenty-two participating countries with the Secretariat in New York City, which managed the program as a whole to maintain global consistency of policy and implementation. This model of delegating authority stemmed from the realization that a blueprint approach to selecting Fellows could not be replicable or effective across the diverse human geographies, cultures, educational systems, and socio-economic settings of the IFP countries. From the outset, the Secretariat worked with its local partners to pilot-test, refine, and evaluate approaches for defining, reaching, and selecting IFP target groups. The resulting system was a fine-tuned interplay of local and global features, policy parameters, and implementation strategies. The selection was a local process, with final authority vested in national selection bodies. Once local selection committees had made their decisions, lists of "Fellows-designate" were reviewed by the Secretariat to ensure overall consistency without overriding the national committee process. The Secretariat also monitored the overall performance of the program and collected relevant information from all the participants. Thus, in 2007, the Secretariat instituted an Alumni Census, which compiled the Alumni data provided directly by the International Partners and was, therefore, based on a head count rather than voluntary survey responses. Starting in 2007, a joint CHEPS-IFP Alumni Survey has been carried out annually.

The Secretariat was in operation in 2001 - 2013, headed by Executive Director Joan Dassin. Joan coordinated the initial design process for IFP, which began in December 1999, and assumed the position of IFP Executive Director when the organization was created in April 2001. She was responsible for overall coordination and evaluation of the program worldwide, worked closely with several outside consultants on program communications and also oversaw all aspects of program implementation in Latin America. The Secretariat staff also included Mary Zurbuchen (Director for Asia and Russia), Rob Oppegard (Director of Finance & Administration), Barbara Wanasek (Grants Manager), Alan Divack (Senior Project Manager, Archives and Knowledge Management), Diana Whitten (Director of Communications), Rachel Clift (Communications Officer), Daniel Reisner (Multimedia and Archives Officer) and Adriana Thoen (Administrative Manager).

The Secretariat archival records on paper comprise 160 l.f.; its large archive of digital materials (over 3.5 TB) includes administrative and program files, a multimedia library and digitized audiovisual materials.