Oropouche virus (OROV) causes outbreaks of febrile illness in areas of South and Central America and we recently identified it in Ecuador for the first time, using metagenomic sequencing. The genome sequence data revealed that the Ecuadorian strain of the virus was not detected using a published qRT-PCR, as it differed genetically at the binding site of the reverse primer. To address this, we developed a modified qRT-PCR that showed increased sensitivity for the Ecuadorian strain. This test detected OROV infection in 6 out of 196 febrile patients from Esmeraldas, Ecuador in 2016. OROV was isolated from positive patient samples, viral genome sequences were compared to publicly available OROV sequences. This revealed that the Ecuadorian cases are genetically distinct, suggesting that local transmission of the virus should not be ruled out. This work highlights the need for a better understanding of OROV dynamics in Ecuador and surrounding areas, the importance of considering OROV as a cause of fever in Ecuadorian patients and the possibility of selectively using metagenomic sequencing in parallel to traditional molecular techniques in patient testing.