MicroRNAs (miRNAs) are short RNA gene regulators typically produced from primary transcripts that are cleaved by the nuclear microprocessor complex, with the resulting precursor miRNA hairpins exported by exportin 5 and processed by cytoplasmic Dicer to yield two (5p and 3p) miRNAs. Here, we document microprocessor-independent 7-methylguanosine (m7G)-capped pre-miRNAs, whose 5′ ends coincide with transcription start sites and 3′ ends are most likely generated by transcription termination. By establishing a small RNA Cap-seq method that employs the cap-binding protein eIF4E, we identified a group of murine m7G-capped pre-miRNAs genome wide. The m7G-capped pre-miRNAs are exported via the PHAX-exportin 1 pathway. After Dicer cleavage, only the 3p-miRNA is efficiently loaded onto Argonaute to form a functional microRNP. This unusual miRNA biogenesis pathway, which differs in pre-miRNA synthesis, nuclear-cytoplasmic transport, and guide strand selection, enables the development of shRNA expression constructs that produce a single 3p-siRNA. Display omitted •Microprocessor-independent Dicer-dependent 5′ m7G-capped pre-miRNAs are identified•The 5′ and 3′ ends of m7G-capped pre-miRNAs are generated directly by transcription•Exportin 1 exports m7G-capped pre-miRNAs•m7G-capped shRNA expression vectors express a single siRNA A microprocessor-independent pathway distinct from canonical miRNA biogenesis generates 7-methylguanosine (m7G)-capped pre-miRNAs whose 5′ ends coincide with transcription start sites.