The MIT-Portugal Program Collaboration is based on a contractual arrangement between MIT and the Portuguese Science and Technology Foundation (FCT).

FCT will include a Director of the MIT Portugal Program who reports to the FCT President and who will direct all of the activities that FCT agrees to undertake and/or support with MIT. The Portugal Program at MIT will be led by an MIT faculty member who serves as "Director" and will typically hold an appointment in the Engineering Systems Division, which is serving as the lead unit at MIT.

The program governance structure includes a program governing committee responsible for policy oversight with respect to overall objectives of the relationship as well as approval of the annual plan and budget allocation for the proposed activities in the annual plan; a Program Operating Committee responsible for developing and initially approving annual plans in the focus areas; and an external review committee which will review and comment on the Annual Plan, and evaluate the Program based on the specified Program objectives.

The Program Governing Committee and Program Operating Committee will, simultaneously with their respective review and approval of MIT’s annual plan, apply the same review and approval process to the annual plan of each Portuguese institution that is committing to collaborate with MIT on a project or program.