Background and objectives: Functional electrical stimulation (FES) has shown good results in improving static and dynamic sitting balance in persons with spinal cord injuries. There is limited information about how regular surface FES combined with therapeutic exercise (TE) affect dynamic sitting balance and muscle tone. The objective of this study was to evaluate the effectiveness of a six-week physical therapy program consisting of FES and TE on muscle tone and sitting balance in persons with spinal cord injury (SCI). It was also important to explore the relationship between muscle tone and dynamic sitting balance. The third objective was to assess the change of characteristics over a six month period, when no intervention was carried out. Material and methods: Five men with SCI were alternately allocated to two study groups: SCI_FES+TE and SCI_TE. Eight healthy control group participants were recruited to collect reference data. SCI participants’ intervention lasted for six weeks in their homes. SCI_FES+TE conducted exercises with FES applied on erector spinae (ES) and rectus abdominis (RA) muscles. SCI_TE conducted exercises only. Muscle oscillation frequency (MOF; characterizing muscle tone) and limits of stability (LOS; characterizing sitting balance) were measured. A crossover study design was used. The time between the initial intervention and the crossover was seven months (ClinicalTrials registration ID NCT03517787). Results: MOF in SCI_FES+TE increased by 6.0% for ES and 6.1% for RA muscles. LOS of flexion increased 30.1% in SCI_FES+TE. Increase in lateral directions was similar for both study groups. Moderate to high negative correlation was found between MOF and LOS. After seven months, MOF of ES decreased 0.8%, MOF or RA decreased 1.4%, LOS of flexion decreased 31.9%, and LOS of lateral flexion to the left decreased 46.4%. Conclusions: The six-week therapy program combining FES and TE increased trunk muscle tone and dynamic sitting balance in flexion more than TE alone. Higher antagonist muscle tone negatively affects dynamic sitting balance and center of pressure (COP) trajectory distance in various directions. After seven months, a slight decline in trunk muscles tone values and an extensive decrease in sitting balance values were noticed.