Influenza D virus (IDV) was first reported in pigs in the USA, and since then the virus has become a public health issue. In Nigeria, no work has been done on IDV despite the manifestation of influenza-like illness in cattle. This study aimed at molecular surveillance of IDV in cattle in Lagos. Prospective epidemiological investigation was initiated in a large commercial farm market where animals in open pens are reared, sold, and butchered under poor hygienic conditions without adequate biosecurity measures. A total of 80 nasopharyngeal swabs were collected between October and November 2021. The samples were extracted using an RNA purification kit (NIMR). RNA extracts were amplified following a two-step PCR using FIREScript RT cDNA synthesis kit (Solis Biodyne, Estonia), followed by PCR OneTaq Quick-load 2x master-mix (NEB, UK) in a Rotor-Gene thermocycler (Qiagen, Germany). Amplicons were detected using a 1.5% Gel electrophoresis. IDV was detected in 26/80 (32.5%) cattle. Sick animals showed 65% (17/26) almost double burden of IDV higher than 34.6% (9/26) in a healthy population, including 88.2% (15/17) Cattle with diarrhoea and 11.8% (2/17) with nausea having IDV. Bull recorded more than twice, 18/26 (69.2%) incidence by gender compared to Cow. Age prevalence showed 62.23% (18/26) highest detection in cattle of 4 years old, followed by 23.07% (6/26) in 5 years old, while the lowest 7.69% (2/26) was recorded in 3 years old. This study showed the first molecular detection of IDV in Nigeria and West Africa sub-region to the best of our knowledge. It underscores the need for continuous surveillance of IDV at the animal-human interface.