The aim of this study was to examine the impact of grazing management and other risk factors (age, treatment practices) on seasonal activity of gastrointestinal (GI) parasites in goats. Goat flocks naturally infected with GI parasites reared on four Lithuanian farms representing different management regimes were examined during the grazing season in 2011/2012. On three farms the adult goats were grazed in different ways on open pastures (with or without supplementary feeding) or tethered. On one farm all animals were kept indoor (zero-grazing). On each farm, samples were collected at monthly intervals from 13–15 adult and 10 kids. The results showed that grazing of adult goats with feed supplementation or kept indoor, shed the lowest number of strongyle eggs when compared to those kept on pasture (P < 0.05). Delayed turnout and zero-grazing significantly reduced excretion of strongyle eggs but increased the output of oocysts when compared to those grazed on set-stocked pasture together with adult goats. The most prevalent genus on all farms and in both age groups of goats were Teladorsagia spp. This study demonstrates that goats are infected with mixed species of parasites, but proportions of these parasites differed in different grazing management systems. The grazing management, age and season were all major factors that had an impact on GI parasite infection.