Most proteins carry out their functions by participating in protein complexes. Recently, miRNAs were identified as promising post-transcriptional regulators that influence a large proportion of genes in higher eukaryotes. We aim to understand the role of miRNAs in the regulation of human proteins that are present in protein complexes. Here, we show that robust regulation by miRNA is absent in human complex-forming proteins. Moreover, the numbers of miRNA hits cannot direct the evolutionary fate of complex-forming proteins independently. However, the duplicated complex-forming proteins having a severe effect on organismal fitness are profoundly targeted by miRNA, probably to reduce the chances of dosage imbalance.