The basolateral amygdala (BLA) and the nucleus accumbens core (NAcc) share some similar behavioral functions, such as associative learning, Pavlovian to instrumental transfer, and choice behavior. However, their prefrontal anatomical inputs have not been well characterized before, especially the collateral projections. In this study, we analyzed the distribution and collateralization of projections to the BLA and the NAcc from the prefrontal cortices (PFC), including the prelimbic (PL) and the infralimbic (IL) divisions of the medial prefrontal cortex (mPFC) and the subregions of the orbitofrontal cortex (OFC), such as the medial OFC (MO), the lateral OFC (LO), and the ventral OFC (VO). Double retrograde tracing approach was used, in which Cholera toxin subunit B conjugated with the Alexa Fluor 488 (CTB-AF488) or Alexa Fluor 594 (CTB-AF594) were unilaterally injected into the BLA and the NAcc, respectively, in male Long-Evans rats (n = 6). Among the sampled neurons, prefrontal projection to the BLA or the NAcc is more robust on the ipsilateral side, and more robust from the PL, the IL, and the MO compared to from the LO and the VO. The majority of the projections from the PFC to the BLA and/or the NAcc are confined in deep layer. In addition, for each of the prefrontal areas, about 15–25% BLA-projecting neurons send collateral projections to the NAcc, and vice versa. In conclusion, our data suggested that prefrontal control over the BLA and the NAcc is not entirely independent. The functional importance of the collateral projections awaits further examination.