Altitudinal distributions, population structures and seasonal dynamics of tick fauna at three localities in Continental Croatia (Medvednica and Papuk) and an alpine biogeographic region (Gorski Kotar) were studied. Sampling of questing ticks was performed twice a year (spring and autumn, from 2019 to 2021) at different altitudes (200, 400, 600, 800 and 1000 m above sea level) using the flagging method. In total, 2942 ticks (53.9% larvae, 40.1% nymphs, 6.0% adults) were sampled and 2937 (99.83%) were determined as Ixodes ricinus, 4 (0.14%) as Haemaphysalis concinna and 1 (0.03%) as Ixodes frontalis. Ixodes ricinus was the only species found at all altitudes and sampling sites. The highest tick abundance was recorded at higher altitudes (800–1000 m asl.) on Medvednica and in Gorski Kotar within mixed forests of European beech and European silver fir, while on Papuk most of the ticks were sampled at lower altitudes (200 m asl.) in Sessile oak forest. From 27 pools containing 305 ticks, 1 (3.7%) was positive for Borrelia burgdorferi sensu lato infection. Borrelia burgdorferi s.l. was detected in 20% (1/5) of the pools containing nymphs and adults collected in Gorski Kotar (600 and 800 m asl.). Sequencing of the ospA gene and phylogenetic analysis revealed the presence of the Borrelia burgdorferi sensu stricto genotype.