Background: Studies have suggested that musculoskeletal symptoms increase after natural disasters. The Great East Japan Earthquake (GEJE) and accompanying tsunami placed a huge financial burden on the local population. This study determined whether subjective economic hardship influenced the new onset of neck pain (katakori) in the chronic phase after the GEJE. Methods: This study used longitudinal data from 1359 adults who had responded to the self-report questionnaire at 2 and 3 years after the GEJE. New-onset neck pain was defined as neck pain absent at 2 years and present at 3 years. Subjective economic hardship at 2 years after the GEJE was categorized into 4 groups: “normal,” “a little bit hard,” “hard,” and “very hard.” Multiple logistic regression analysis was used to estimate the odds ratio (OR) and 95% confidence interval (CI) in order to examine the association between subjective economic hardship and new-onset neck pain. Results: Among the participants, 12.9% (n = 175) reported new-onset neck pain. A significantly higher rate of new-onset neck pain was observed in participants who considered their subjective economic hardship to be “hard” (OR = 2.10, 95% CI = 1.34–3.30) or “very hard” (OR = 3.26, 95% CI = 1.83–5.46; p for trend <0.001) compared with those who considered their hardship to be “normal.” Conclusions: Subjective economic hardship was significantly associated with new-onset neck pain in the chronic phase of the GEJE. (228/300).