Purpose Global Perceived Effect (GPE) is a commonly used outcome measure for musculoskeletal conditions like neck pain; however, little is known regarding the factors patients take into account when determining their GPE. The overall objective of this work was to describe the thematic variables, which comprise the GPE from the patient's perspective. Methods This was a mixed-methods study in which qualitative data were collected within a randomized clinical trial assessing exercise and manual therapy for chronic neck pain. A consecutive sample of 106 patients who completed the trial intervention took part in semi-structured interviews querying the meaning of GPE. Quantitative measures were collected through self-report questionnaires. Interview transcripts were analyzed using content analysis to identify themes, which were then quantified to assess potential relationships. Results A model of GPE for chronic neck pain emerged comprised of five main themes: neck symptoms (cited by 85 %), biomechanical performance (38 %), activities of daily living (31 %), self-efficacy (10 %), and need for other treatment (6 %). Influencing factors included those contributing to GPE: treatment process (64 %), biomechanical performance (51 %), self-efficacy (16 %), and the nature of the condition (8 %). Factors, which detracted from GPE or prevented recovery included perceived nature of condition (58 %), required daily activities (10 %), lack of diagnosis (5 %), and history of failed treatment (5 %). Conclusions GPE appears to capture chronic neck pain patient perceptions of change in different domains important to their individual pain experiences that may not be captured by other outcome instruments. Thus, GPE is a suitable patient-oriented outcome that can complement other measures in research and clinical practice. Importantly, many chronic neck pain patients believe it impossible to reach complete recovery because of a perceived intractable aspect of their neck condition; this has important implications regarding long-term disability and healthseeking behaviors.