Super Inductive System (SIS) stimulation of spastic limbs by tissue-induced electromagnetic field may have the effect of reducing spasticity and improving functionality in patients with post-stroke spasticity. The aim of the study was to evaluate two different protocols for the application of SIS on upper limb spasticity after stroke. We included 60 patients with post-stroke upper limb spasticity, who were randomized into two groups: the study group, with a 9 min application protocol (1 min for agonist muscles, 8 min for antagonistic muscles); and the control group, with an 8 min protocol applied only to the antagonistic muscles. The duration of therapy was 10 days, and the results were assessed using the Modified Ashworth Scale (MAS) and the Barthel Index. Both the MAS and the Barthel Index improved significantly after 10 days of treatment (p < 0.001), but 30 days after the completion of therapy, there was an attenuation of the effects in both study groups. The study group had a significantly higher percentage of patients with improved MAS after 10 days (p = 0.004) and within 30 days (p < 0.001) than the control group. An SIS protocol applied on both agonist and antagonist muscles has a more pronounced and longer lasting spasticity-reducing and improved functionality effect than its application on only antagonistic muscles.