Background Tunga penetrans (Insecta, Siphonaptera, Tungidae) causes severe morbidity among heavily infected humans and animals in Latin America and sub- Saharan Africa. The clinical pathology of tungiasis in animals has never been studied systematically. Methods This was a cross-sectional study conducted between January to March 2015, aimed at describing tungiasis-associated clinical pathology in 121 and 20 T. penetrans-infected pigs and dogs, living in nine and five endemic rural villages respectively located in Bugiri District, Busoga, Uganda. Results The parasite load of infected animals ranged from one to 246 (median 8) and one to eight (median 2) in pigs and dogs, respectively. In pigs 99.3 % and in dogs 100 % of the lesions were located on feet. In pigs, hind legs were significantly more affected than front legs (90.9 % vs. 57.9 %; p = 0.002) and also had more lesions than the front legs (median 5 vs. 1; p = 0.0001). However, in dogs localization of lesions between front and hind legs never differed significantly (front, 50 % vs. hind, 65 %; p = 0.51) and so were the number of lesions (median front = 0.5 vs. median hind = 2; p = 0.7). Acute and chronic clinical pathology coexisted. The most common disease manifestations in pigs were hoof wall erosions (68.6 %), tissue necrosis of hoof wall and skin (66.1), pain at infection sites (47.9 %), hoof deformity (45.5 %), fissures (44.6 %) and edema (44.6 %). In dogs, tungiasis mainly presented with pain at attachment site (80 %), ulcers (55 %), necrosis (30 %) as well as hyperemia and edema (both 15 %). One pig had lost dew claws while two had loose detaching claws. Despite a lower number of sand fleas, a higher proportion of infected dogs (20 %) than pigs (5.8 %) exhibited functional limb use difficulties (p = 0.05). Conclusions The pattern of clinical manifestations in pigs and dogs were very similar to those reported from affected humans and rats. The important morbidity associated with animal tungiasis makes the disease a serious veterinary health problem in sub-Saharan Africa warranting treatment and control for optimal animal production.