Babesiosis, theileriosis, anaplasmosis, and heartwater are tick-borne diseases that threaten livestock production in sub-Saharan Africa including Burkina Faso and Benin. For over a decade, these two bordering countries have been facing an invasion of the livestock by the tick Rhipicephalus microplus, a major vector for babesiosis, accidentally introduced in Benin in 2004. The molecular identification of tick-borne pathogens in this border area is of particular interest due to animals seasonal migration between the two countries. In this survey, epidemiological features of ticks and tick-borne pathogens in cattle were investigated to compare the eastern Burkina Faso, corresponding to a seasonal migration departure zone, and the northern Benin, which represents a seasonal migration arrival zone. Ticks and peripheral blood were collected from a total of 946 cattle in the two areas. Ticks were morphologically identified and the DNA samples from bovine blood and ticks were analysed by Reverse Line Blot (RLB) hybridization process. A total of 2856 ticks were collected on 490 cattle in Burkina Faso, eight tick species were identified, while 3583 ticks were collected on 456 cattle in North Benin with nine tick species identified. The invasive tick, R. microplus was not found in eastern Burkina Faso, but its spread farthest north in Benin is reported. Six tick-borne pathogen species were found in cattle blood both in eastern Burkina Faso and in northern Benin. Ranked in decreasing order of overall prevalences, they are: Theileria mutans (91.1%), Theileria velifera (77.8%), Babesia bigemina (10.9%), Anaplasma marginale (4.2%), Babesia bovis (3.3%), and Theileria annulata (1.8%). To the best of our knowledge, this survey represents the first report of T. velifera and T. annulata in the region. Overall, the TBP prevalences were significantly higher in northern Benin than in eastern Burkina Faso, indicating a higher parasitological risk in this area.