Co-chaperone required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Acts as a co-chaperone via its interaction with HSP90 and is required for the piRNA amplification process, the secondary piRNA biogenesis. May be required together with HSP90 in removal of 16 nucleotide ping-pong by-products from Piwi complexes, possibly facilitating turnover of Piwi complexes (By similarity). Interacts with HSP72/HSPA2 and CLTC. Interacts with GAPDH; leading to inhibit GAPDH catalytic activity. Interacts (via TPR repeats) with HSP90 (By similarity). Does not localize to pi-bodies. Localizes to meiotic chromosome cores and regions of homologous chromosome synapsis (By similarity). Specifically expressed in testis and sperm. Defects in FKBP6 may be a cause of stallion sterility due to defects in acrosomal reaction. Disease susceptibility is associated with variants affecting the gene represented in this entry (PubMed:23284302). Belongs to the FKBP6 family. Although it contains a PPIase FKBP-type domain, does not show peptidyl-prolyl cis-trans isomerase activity.