In 2009, the Panama City Project Center was established for MQP students working with the Panama Canal Authority on civil engineering projects related to the maintenance and operation of the Panama Canal – channel dredging, dam and spillway design, water quality issues at Gatun Lake, developing shoreline management plans, etc. In 2015, the site was expanded to accept IQP students. Projects have generally focused on the overlapping themes of sustainability (particularly in the interconnections between food, energy, and water) and income inequality (Panama has one of the most unequal distributions of wealth in the developed world). In 2017, for the first time, the Panama City Project Center hosted a full complement of IQP students (6 teams accompanied by two faculty).

Past projects have included working with Cope Airlines, the national air carrier of Panama, to reduce bird strikes on planes at Tocumen International Airport without negatively affecting the surrounding community; introducing composting systems in the facilities of the City of Knowledge, where students are housed; and working with Footprint Possibilities to expand access to drinking water for the community in the Maser Nega slum on the outskirts of Panama City.