Neuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing anti-neurogenic genes. How these miRNAs function after the onset of the transcriptome switch to a neuronal fate remains unclear. Here, we identified direct targets of miRNAs by Argonaute (AGO) HITS-CLIP as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function. Overall design: Neonatal fibroblasts were converted using miR-9/9*-124 or control, miR-NS, into neurons (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015). Cells were collected to identify transcripts with AGO-enriched binding during reprogramming. The two miR-NS and miR-9/9*-124 timepoints were processed as two biological replicates.