Neural epidermal growth factor-like 1 protein (NELL1) is the second most common target antigen in membranous glomerulonephritis (MGN). However, data regarding the clinicopathological characteristics of NELL1-associated MGN are limited owing to its low prevalence. This study examined the prevalence and clinicopathological characteristics of NELL1-associated MGN in a Japanese cohort. Additionally, we compared the clinicopathological features of NELL1-positive MGN, phospholipase A2 receptor 1 (PLA2R1)-positive MGN, and MGN negative for all three antigens (NELL1, PLA2R1, and thrombospondin type-1 domain-containing 7A). Among 257 consecutive patients pathologically diagnosed with MGN at two centers in Japan, 24 (9.3%) were immunohistochemically positive for NELL1. Clinically, patients with NELL1-positive MGN were significantly older (p < 0.001) and had a higher frequency of bucillamine use (vs PLA2R1-positive MGN, p < 0.01). Histologically, NELL1-positive MGN exhibited significantly lower detection of spikes and crater formation (p < 0.001), higher prevalence of segmental spike distribution (vs PLA2R1-positive MGN: p < 0.001), and higher prevalence of stage I cases on electron microscopy (p < 0.01). There were no significant differences in the prognoses among the three groups. The characteristic histological feature of segmental distribution in NELL1-positive MGN may be related to bucillamine use and the early phase of the disease. Further investigations with larger numbers of patients may offer further insight into the prognosis of patients with NELL1-positive MGN.