This article presents datasets associated with the research article entitled "Intravitreal gene therapy protects against retinal dysfunction and degeneration in sheep with CLN5 Batten disease" (Murray et al., [1]). The neuronal ceroid lipofuscinoses (NCL; Batten disease) are a group of fatal inherited diseases caused by mutations in a number of CLN genes that lead to degenerative and fatal encephalopathies in children. Naturally-occuring sheep models of NCL exist. Affected sheep share the clinical and pathological features of the human disease, including retinal degeneration. Electroretinography (ERG) was employed to characterise the physiological changes in the degenerating retina of CLN5 and CLN6 forms of ovine NCL. ERGs were performed every two months from 3 to 17 months of age in 11 NCL affected (6 CLN5-/ - and 5 CLN6-/- ) sheep and 12 clinically normal heterozygous controls (6 CLN5+/ - and 6 CLN6 +/-) under three different adaptation conditions. A-wave and b-wave amplitudes were collected from each eye using the Eickemeyer Veterinary ERG system. These are the first longitudinal datasets assessing the progression of retinal degeneration in ovine NCL, aiding in characterisation of the disease process and providing insight into optimal therapeutic windows for subsequent studies.