Many women suffer from back pain and experience activity limitation post-partum. To our knowledge the physiological factors and physiotherapy related to back pain post-partum have received limited evaluation and the effectiveness of specific physiotherapeutic approaches to exercise should be tested. In addition, there has been limited research on kinesiophobia in women with back pain post-partum. The purpose of the current study was to test the influence of specific trunk muscle training on pain, activity limitation and kinesiophobia in 10 subjects with back pain post-partum. The treatment consisted of specific deep muscle training of the transversus abdominus and multifidus muscles. Pain was rated based on the visual analogue scale (VAS) and pain drawings. Activity limitation was recorded using the Disability Rating Index. Kinesiophobia was evaluated using the Swedish version of the Tampa Scale for Kinesiophobia. An A-B-A single-subject research design was used and a number of measurements were obtained during each phase. The analysis consisted of a visual inspection and a two standard deviation band test (2-SD). The visual analysis showed a trend towards reduced pain and activity limitation for all 10 subjects. The 2-SD test showed mixed results among all subjects. In addition, all subjects reported kinesiophobia before and after treatment. Individual specific deep muscle training of the transversus abdominus and multifidus muscles reduced pain and activity limitation in women with back pain post-partum. Further research is needed to determine more precisely how kinesiophobia affects women with back pain post-partum.