Due to the lack of recombination, the male-specific region of the Y chromosome (MSY) is a unique resource for tracking the genetic history of populations. The MSY is also enriched for large, nearly identical repetitive regions known as amplicons, which harbor many of the genes essential for spermatogenesis. In humans, sequence diversity on the unique segment of the MSY is greatly reduced compared to the autosomes, an observation consistent with the action of strong selection. Here, we analyze 9 chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two Pan paniscus male whole-genome sequences to assess Y chromosome nucleotide and ampliconic copy-number diversity across the Pan genus. In total, we identified 23,946 Pan spp. SNVs across 4.2 million callable sites. Comparisons with autosomal, X chromosome, and mitochondrial sequences from the same samples indicate that nucleotide diversity on the chimpanzee MSY is reduced relative to neutral expectations with an equal sex ratio. Additionally, the estimated common chimpanzee Y chromosome TMRCA (0.44 mya [0.31-0.56]) is half the age of the mitochondria TMRCA (0.97 mya [0.65-1.35]), indicating an unequal sex ratio or Y chromosome selection in the common chimpanzee ancestral population. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of the testis-expressed genes RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.