Unsaturated fatty acids are attractive alternatives to fossil‐based materials as a source of hydrocarbons, but potential applications are limited by the preset chain length of 16–20 carbon atoms. However, if the double bond can be randomly moved along the chain, subsequent bond‐breaking operations such as ethenolysis or oxidative cleavage will give rise to products with chain lengths ranging from 2 to 18 carbon atoms. A process for the double bond isomerization of rapeseed oil methyl esters in a flow‐through reactor using zeolites as the catalyst is herein disclosed. Using H‐mordenite as the catalyst at a flow of 0.125 mL min−1 at 290 °C, near equilibrium isomerization is reached with up to 49% recovery of linear monomeric products after 5 h and up to 44% after 48 h. The main side products are oligomers (3%–15%) and skeletal isomerization products (10%–23%). Practical applications: With a suitable follow‐up modification addressing the double bond (metathesis, ozonolysis, oxidative cleavage), the product mixtures of double‐bond positional isomers can be used in the production of short‐chain base chemicals. In repetitive combination with metathesis catalysis, biofuels with customized chain length distributions can be generated.