The aim of the study was to use serological techniques to determine the seroprevalence and phylogenetic position of Toxoplasma (T.) gondii infecting goats of Malakand division of Pakistan. Toxoplasma gondii is an apicomplexan protozoan parasite infecting one-third of the population of the world, including humans, animals, birds, etc. Still, no information on T. gondii infection in goats regarding serological and the phylogenetic investigations are reported from the Malakand division. Randomly, 450 goat blood samples were collected from various districts. Risk factor information was recorded from the owners by questionnaire. ELISA test was used for the detection of T. gondii infection in goats, and positive samples were subjected to a PCR test using the ITS-1 gene. The overall seroprevalence of T. gondii infection in goats was 23.11% (104/450). The prevalence of parasite was higher in female goats (25.69%), non-aborted goats (25.85%), open grazing animals (25.38%), and the summer season months of June (42.55%), July (30.23%), and August (31.14%). Among different districts, the highest seroprevalence was found in district Lower Dir (38%). The BLAST analysis of partial sequences of PCR products of T. gondii based on ITS-1 showed 99% similarities with reported genotypes found in cattle and goats in Punjab and Brazil. It was concluded that a large number of goats may be positive for T. gondii in the study area. Risk factors like gender, age, area, etc. are strongly associated with the infection, which may play a key role in the spreading of the disease in animals and humans as well.