Painful no. Uncomfortable? It depends on the individual. In the great majority of patients TMS is well tolerated with only minor discomfort on the scalp where TMS is applied. Most people describe TMS as a light to moderate tapping sensation where the coil is being applied. The sensation of the pulse may feel similar to a TENS unit.
The reason for this is that there are several nerves in the scalp where TMS is being applied. Naturally some of these nerves will also be lightly stimulated by the TMS coil as they are also conductive and will pick up the pulse. This is the part of the TMS that you can feel. You cannot feel TMS in your brain, as the brain has no pain receptors itself.
And even though stimulation of the scalp nerves may cause some discomfortat at first, this too subsides as the patient progresses through treatment.