This work reports the synthesis of Pd-based alloys of Co and their evaluation as anode materials in a microfluidic formic acid fuel cell (μFAFC). The catalysts were prepared using the impregnation method followed by thermal treatment. The synthesized catalysts contain 22wt.% Pd on multiwalled carbon nanotubes (Pd/MWCNT) and its alloys with two Co atomic percent in the sample with 4 at.% Co (PdCo1/MWCNT) and 10 at.% Co (PdCo2/MWCNT). The role of the alloying element was determined by XRD and XPS techniques. Both catalysts were evaluated as anode materials in a μFAFC operating with different concentrations of HCOOH (0.1 and 0.5M), and the results were compared to those obtained with Pd/MWCNT. A better performance was obtained for the cell using PdCo1/MWCNT (1.75mWcm−2) compared to Pd/MWCNT (0.85mWcm−2) in the presence of 0.5M HCOOH. By means of external electrode measurements, it was also possible to observe shifts in the formic acid oxidation potential due to a fuel concentration increment (ca. 0.05V for both PdCo1/MWCNT and PdCo2/MWCNT catalysts and 0.23V for Pd/MWCNT) that was attributed to deactivation of the catalyst material. The maximum current densities obtained were 8mAcm−2 and 5.2mAcm−2 for PdCo2/MWCNT and Pd/MWCNT, respectively. In this way, the addition of Co to the Pd catalyst was shown to improve the tolerance of intermediates produced during formic acid oxidation that tend to poison Pd, thus improving the catalytic activity and stability of the cell.