This single group, randomized, cross-over study explored whether manual therapy alters motor tone of deep thoracic back muscles by examining resting electromyographic activity (EMG) after 2 types of manual therapy and a sham control intervention. Twenty-two participants with thoracic spinal pain (15 females, 7 males, mean age 28.1 ± 6.4 years) had dual fine-wire, intramuscular electrodes inserted into deep transversospinalis muscles at a thoracic level where tissues appeared abnormal to palpation (AbP) and at 2 sites above and below normal and non-tender to palpation (NT). A surface electrode was on the contralateral paraspinal mass at the level of AbP. EMG signals were recorded for resting prone, two 3-s free neck extension efforts, two 3-s resisted maximal voluntary isometric contractions (MVIC), and resting prone before the intervention. Randomized spinal manipulation, counterstrain, or sham manipulation was delivered and EMG re-measured. Participants returned 1 and 2 weeks later for the remaining 2 treatments. Reductions in resting EMG followed counterstrain in AbP (median decrease 3.3%, P = 0.01) and NT sites (median decrease 1.0%, P = 0.05) and for the surface electrode site (median decrease 2.0%, P = 0.009). Reduction in EMG following counterstrain during free neck extension was found for the surface electrode site (median decrease 2.7%, P < 0.01). Spinal manipulation produced no change in EMG, whereas counterstrain technique produced small significant reductions in paraspinal muscle activity during prone resting and free neck extension conditions. The clinical relevance of these changes is unclear.