Tumors, especially neuroendocrine tumors (NETs), can cause adverse effects on human health. The expression and significance of Ki-67 and caspase-3 in NET remain to be further explored. Everolimus is an important drug used for the treatment of NETs. In this study, we aimed to investigate whether everolimus exerts anti-tumor effects by suppressing the expression of Ki-67 and caspase-3 in NET. Tumor (different developmental stages) and adjacent tissues were collected from patients with NET. The expression of Ki-67 and caspase-3 were detected in 244 paraffin sections of NET using immunohistochemistry. RT-PCR and western blot were used to detect the expression of Ki-67 and caspase-3 at mRNA and protein levels, respectively. The patients (N = 244) were randomly divided into everolimus-intervention and control groups. RT-PCR and western blot were used to measure the expression changes of Ki-67 and caspase-3 before and after everolimus treatment. The rates of Ki-67 expression in NET grades 1-6 were 14.2, 22.1, 37.5, 59.9, 69.9, and 77.8%, respectively. The difference between the groups was significant. The rates of caspase-3 expression in NET grades 1-6 were 28.6, 33.3, 31.3, 60.0, 80.0, and 88.9%, respectively, and the difference between groups was significant. Moreover, the expression of Ki-67 and caspase-3 showed a significant negative correlation. The expression of Ki-67 decreased while that of caspase-3 increased after everolimus treatment. In conclusion, the decrease in Ki-67 expression and increase in caspase-3 expression after everolimus treatment indicated that everolimus exerted its anti-cancer effect by regulating the expression of Ki-67 and caspase-3.