Joubert syndrome (JS) is a rare genetic ciliopathy characterized by the aplasia or malformation of the midbrain and or hindbrain structures. It usually manifests during the early stages with nonspecific neurological symptoms that progress to involve multiple systems. Its presentation similarity to other neurological disorders makes the diagnosis difficult, hence causing a delay in treatment and worse prognosis due to complications. If undiagnosed during childhood, it often presents during adolescence with the most common complication of acute kidney injury due to nephronophthisis. Here, we present a case of JS in late adolescence with renal complications and other neurological abnormalities. We aim to emphasize the importance of its early diagnosis by physicians in childhood to prevent further complications. It also highlights the possible diagnostic value and significance of brain imaging in the early stages when only mild mental retardation signs may be the only clues.