The Eucommia ulmoides rubber (EuR) is a naturally occurring long-chain trans-1,4-polyisoprene with extensive applications but high production costs. Previous studies suggest that the Eucommia farnesyl diphosphate synthase 5 (EuFPS5) alone is capable of catalyzing the biosynthesis of EuR. As the most high-yielding cis-polyisoprene-producing plant species with a cost-effective latex harvesting system, Hevea brasiliensis exhibits the potential to produce EuR at a lower cost. Via Agrobacterium-mediated transformation, this study generated a transgenic Hevea line overexpressing EuFPS5 (EuFPS5oe). The EuFPS5oe Hevea plants exhibited slightly wrinkled leaves, but no significant difference in growth vigor compared to the wild type control (WT). 1H and 13C nuclear magnetic resonance (NMR) analyses indicated that the rubber of 1-year-old EuFPS5oe plants was identical to that of WT, suggesting that EuFPS5 alone is not sufficient to catalyze the biosynthesis of EuR in Hevea. However, compared to the WT, EuFPS5oe plants showed significantly increased rubber content in the leaves, while the rubber molecular weight in the latex decreased. LC-MS/MS analysis showed that the EuFPS5oe latex contained a comparable level of IPP, but a significantly higher level of FPP than the WT. Taken together, our study suggests a role for EuFPS5 in the biosynthesis of FPP in Hevea, provides in vivo evidence that under limited IPP supply, higher FPP level increases rubber production but decreases rubber molecular weight, and thus lays a foundation for future genetic improvement of natural rubber production in Hevea brasiliensis.