Numerous studies have shown that neurological changes are important findings of tinnitus patients. Previous studies on tinnitus have indicated that patients with pulsatile tinnitus (PT) often show altered baseline brain activity in the resting state. This study used resting-state functional magnetic resonance imaging (rs-fMRI) to investigate changes in spontaneous brain activity among patients with unilateral pulsatile tinnitus in the early stage of disease (less than forty-eight months) and determined the relationship of these changes with clinical data. The PT patients (n = 34) and matched normal control subjects (n = 34) were enrolled in this study. Spontaneous brain activity was revealed by the regional homogeneity (ReHo) and amplitude of low-frequency fluctuation (ALFF) values. Compared with normal controls, the patients with PT had significantly increased ReHo and ALFF in the posterior cingulate cortex, right inferior parietal lobule (IPL) and right cerebellum posterior lobe. The PT group showed increased ReHo in the posterior cingulate cortex (PCC), precuneus, right IPL, right superior frontal gyrus, some occipital areas and part of the right cerebellum posterior lobe. For ALFF, the increased clusters were in the PCC and precuneus and in some areas of the cerebellum posterior lobe, bilateral IPL and inferior frontal gyrus (IFG). Increased PT duration was correlated with increased ALFF in the bilateral inferior frontal gyrus (IFG) and precuneus. An increased THI score was correlated with ReHo and ALFF values in the precuneus. Taken together, the combined study of ReHo and ALFF measurements may yield a more comprehensive neurological pathophysiology framework for PT patients in the early stage of the disease.