(1) Background: Stroke is one of the leading causes of disability. To identify the best treatment strategies for people with stroke (PwS), the aim of the current study was to compare the effects of training on a treadmill with functional electrical stimulation (TT-FES) with training on a treadmill (TT), and to analyze the effects of sequence of training on mobility and the parameters of walking ability. (2) Methods: Prospective, longitudinal, randomized and crossover study, in which 28 PwS were distributed into groups, namely the A-B Group (TT-FES followed by TT) and B-A Group (TT followed by TT-FES), using the foot drop stimulator, and were measured with functional tests. (3) Results: We found improved mobility, balance, non-paretic limb coordination, and endurance only in the group that started with TT-FES. However, sensorimotor function improved regardless of the order of training, and paretic limb coordination only improved in the B-A Group, but after TT-FES. These data indicate that the order of the protocols changed the results. (4) Conclusions: Although biomechanical evaluation methods were not used, which can be considered a limitation, our results showed that TT-FES was superior to isolated training on a treadmill with regard to balance, endurance capacity, and coordination of the non-paretic limb.