Oestrogens play an important role in the development and progression of papillary thyroid carcinoma (PTC) through oestrogen receptor (ER)-α and -β, which may exert different or even opposing actions in PTC. The roles of ERβ in ERα-negative PTC are still not clear. This study investigated the expression dynamics of ERβ1 (wild-type ERβ) and its clinical significance in female ERα-negative PTC patients. ERβ1 expression was detected in thyroid tissues of 136 female patients diagnosed with PTC. The relationships between ERβ1 expression and clinicopathological/biological factors were also analysed in female ERα-negative PTC patients. The total score for ERβ1 was significantly lower in female ERα-negative PTC patients with LNM or ETE when compared to those without LNM or ETE (Z = -2.923, P = 0.003 and Z = -3.441, P = 0.001). Accordingly, the total score for ERβ1 was significantly higher in ERα-negative PTC patients expressing E-cadherin compared to patients negative for E-cadherin expression (Z = -2.636, P = 0.008). The total score was lower in ERα-negative PTC patients positive for VEGF expression compared to those negative for VEGF expression (Z = -1.914, P = 0.056). This preliminary study indicates that reduced expression of ERβ1 in female ERα-negative PTC patients is associated with greater progression of the disease. This may provide insights into the underlying molecular mechanisms of ERβ1 and could help design targeted approaches for treating or even preventing this disease.