Methoxykaolinite is a very popular organo-modified kaolinite. Even though it has a number of interesting properties, this nanohybrid material is still underused in terms of practical applications. In the present study, methoxykaolinite was synthesized and used for the first time as an electrode modifier for Pb(II) determination in various aqueous media. X-ray powder diffractometry (XRD), 13C nuclear magnetic resonance (NMR), and Fourier-transform infrared (FTIR) spectroscopy were used as characterization tools to confirm the presence of grafted methoxy groups in the interlayer space of kaolinite. The electrochemical characterization of methoxykaolinite using the cationic probe Ru(NH3)63+ showed that the modified clay presents favorable interactions with cationic compounds. A methoxykaolinite-modified electrode was applied successfully to the quantification of Pb(II) in aqueous solution. At optimized experimental conditions, the calibration curve in the concentration range 0.025–0.3 μM showed excellent linearity (R2 > 0.99), a sensitivity of 3.36 μA μM–1, and a detection limit of 5.6 nM. This detection limit was 10 times lower than the minimum concentration of Pb(II) authorized in drinking water. The sensor was used also for the determination of Pb(II) in tap, river, and well water samples with only minor loss of sensitivity and recoveries (90±5% to 110±4%). Thanks to the excellent biocompatibility of kaolinite, the sensor was applied for Pb(II) detection in human urine. Recovery in the range 98±8% to 103±6% was obtained when three freshly collected urine samples were spiked with known amounts of Pb(II). These results showed the interesting potential of methoxykaolinite as an electrode modifier for trace-level detection of cations, even in biological samples.