Brain development depends on precise regulation of the balance between neural stem cell proliferation and differentiation. One of the most extensively studied regulators of neural stem cells is Prospero (Pros). In Drosophila larval brains, it had been demonstrated that Pros level must be precisely regulated both spatially and temporally to allow correct brain development. However, how this is achieved remains unknown. In the current study, we directly test whether differential Pros level is regulated at transcriptional or post transcriptional level by performing in situ using a combination of intron and exon probes against pros. We showed although Pros is expressed at low level in neuroblasts (NB) and gradually increase in level in NB progeny over time, pros mRNA is transcribed at equal level in all cells types. This suggests post-transcriptional regulation is likely to be involved in achieving the differential Pros expression. We have identified a novel interactor of pros mRNA - Syncrip. In syp mutants, we observed significantly enlarged optic lobes along with increased number of nBs and increased nB division rate. Both Pros protein and mRNA level are decreased in syp mutants. Surprisingly, our data showed pros transcription is not affected in syp mutants but the stability of the RNA is significantly decreased. Mapping the poly(A) site of pros mRNA revealed pros mRNA harbours two distinct 3’UTR variants, one 3 kb and one 15 kb 3’UTR with the 15 kb UTR being the predominant form. By using in situ probes directly against the 15 kb 3’UTR, we showed the 15 kb variant is only transcribed in mature neurons and this is accompanied by an up-regulation of Pros protein. Interestingly, both forms for pros mRNA are made in syp mutants but not maintained. From the current data, we propose a Syncrip dependent model for regulating differential Pros protein expression through choice and maintenance of 3’UTR variants.