Toxoplasma gondii and Neospora caninum infections in dogs are predominantly manifest asymptomatic. However, these infections can also present highly varied and potentially severe clinical signs. This is due to the parasites’ ability to replicate in a number of cell types within the host organism, with N. caninum exhibiting a particular tropism for the central and peripheral nervous systems, and T. gondii targeting the central nervous system and musculature. In clinical practice, toxoplasmosis and neosporosis are often considered to be closely related diseases, despite their distinct epidemiological, clinical, diagnostic, and therapeutic characteristics. The present review analyses the similarities and differences between these two protozoan infections, since an accurate and timely aetiological diagnosis is essential for establishing effective therapeutic protocols and control strategies.