Increasing evidence suggests that miR-519d-3p functions as tumor suppressor in several tumors, including breast cancer. However, its biological role in the development of colorectal cancer (CRC) still remains unclear. In this study, we found that miR-519d-3p expression level was remarkably down-regulated in CRC tissues samples and cell lines when compared to adjacent normal tissues and cell line by using qRT-PCR detection. Lower miR-519d-3p expression was significantly correlated with TNM stage, tumor size and lymph node metastasis. CRC patients with high level of miR-519d-3p had higher five-year survival rate than those with low expression of miR-519d-3p (p = 0.01178) using Kaplan-Meier analysis. Moreover, multivariate analysis suggested that miR-519d-3p expression might be an independent prognostic indicator for the survival of CRC patients. The in vitro functional analysis, including MTT, flow cytometry and transwell assays indicated that miR-519d-3p overexpression significantly suppressed cell proliferation, migration and invasion, induced cell cycle G0/G1 phase arrest and cell apoptosis of CRC cells. Furthermore, bioinformatics and luciferase reporter assays verified that trophinin associated protein (TROAP) was a direct target of miR-519d-3p in CRC cells. Using Oncomine database analysis, TROAP was confirmed to be upregulated in human CRC tissues. In addition, we found knockdown of TROAP presented similar inhibitory effects of miR-519d-3p overexpression in CRC cell function. In conclusion, miR-519d-3p might be a promising therapeutic strategy against human CRC by directly targeting TROAP.