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Porcine circovirus 4 (PCV4) is a newly identified virus belonging to PCV of the <i>Circoviridae</i> family, the <i>Circovirus</i> genus. We previously found that PCV4 is pathogenic in vitro, while the virus’s replication in cells is still unknown. In this study, we evaluated the N-terminal of the PCV4 capsid (Cap) and identified an NLS at amino acid residues 4–37 of the N-terminus of the PCV4 Cap, ⁴RSRYSRRRRNRRNQRRRGLWPRASRRRYRWRRKN³⁷. The NLS was further divided into two fragments (NLS-A and NLS-B) based on the predicted structure, including two α-helixes, which were located at ⁴RSRYSRRRRNRRNQRR¹⁹ and ²⁴PRASRRRYRWRRK³⁶, respectively. Further studies showed that the NLS, especially the first α-helixes formed by the NLS-A fragment, determined the nuclear localization of the Cap protein, and the amino acid ⁴RSRY⁷ in the NLS of the PCV4 Cap was the critical motif affecting the VLP packaging. These results will provide a theoretical basis for elucidating the infection mechanism of PCV4 and developing subunit vaccines based on VLPs.