Rare earth elements are essential components in renewable energy technologies and advanced functional materials. Despite their critical importance, they are typically present in low concentrations and are in increasingly high demand. Current mining and refining processes are energy intensive and cause significant environmental pollution. Therefore, there is an urgent need for eco-friendly, rapid, and effective analytical methods for their exploration. Traditional detection techniques are often costly, time-consuming, and non-portable. There remains a critical gap in the availability of rapid, sensitive, and economical sensors for rare earth element detection. In this study, we introduce a novel portable electrochemical detection system. This system utilizes a recombinant plasmid constructed using a codon-optimized gene to heterologously express a high-affinity protein that binds rare-earth ions. It integrates a graphene oxide-coated screenprinted electrode with an electrochemical workstation for the detection of rare-earth ions. Given that Yb has widespread applications among rare-earth elements, we selected Yb3+ for detection to validate the sensor’s performance. The developed electrochemical biosensor exhibits a detection limit of 1.617 μM and demonstrates linear response across a concentration range of 10–90 μM (R2 = 0.98). This rare-earth ion electrochemical sensor offers multiple advantages, including high sensitivity, a broad detection range, low cost, ease of use, portability, and potential for field deployment. The materials employed are environmentally friendly, aligning with green production requirements. The proposed method holds promise for practical applications in rare earth mineral exploration.