ABSTRACT Stem cells support tissue maintenance, but the mechanisms that balance the rate of stem cell self-renewal with differentiation at a population level remain uncharacterized. Through investigating the regulation of germline stem cells by two PUF family RNA-binding proteins FBF-1 and FBF-2 in C. elegans , we find that FBF-1 restricts differentiation, while FBF-2 promotes both proliferation and differentiation. FBFs act on a shared set of target mRNAs; however, FBF-1 destabilizes target transcripts, while FBF-2 promotes their accumulation. These regulatory differences result in complementary effects of FBFs on stem cells. We identify a mitotic cyclin as one of the targets affecting stem cell homeostasis. FBF-1-mediated translational control requires the activity of CCR4-NOT deadenylase. Distinct abilities of FBFs to cooperate with CCR4-NOT depend on protein sequences outside of the conserved PUF family RNA-binding domain. We propose that the combination of FBF activities regulates the dynamics of germline stem cell proliferation and differentiation.