The understanding of genetic basis for Philadelphia-negative myeloproliferative neoplasm (MPN) has got much progress in recent years. But the effect of CALR vs. JAK2V617F mutations on the clinical progression and prognosis of primary fibrosis (PMF) remains relatively obscure. In this meta-analysis, we searched Pubmed, Embase, and Web of Science databases for observational studies published until February 2016. Researches that evaluated CALR vs. JAK2V617F mutations on PMF-relevant complications (splenomegaly, leukemic transformation, or thrombosis) and overall survival were selected. Pooled adjust odds ratio (OR), hazard risk (HR), and the corresponding 95 % confidence intervals (CI) were calculated for the CALR-mutant versus the JAK2-mutant categories. Twelve studies involving 435 CALR-mutated and 1116 JAK2V617F PMF patients were analyzed. CALR-mutated patients displayed a lower risk of splenomegaly (OR 0.47, 95 % CI 0.29-0.78) and thrombosis (OR 0.52, 95 % CI 0.29-0.92) but showed no significant difference in the risk of leukemic transformation (OR 0.90, 95 % CI 0.55-1.47) when compared with JAK2-mutated patients. CALR mutation favorably affected overall survival while JAK2 mutation led to poorer survival rate (HR 2.58, 95 % CI 2.08-3.20). This meta-analysis confirmed that a genetic classification of PMF by CALR and JAK2 mutations carried significant prognostic relevance.