The pecan (Carya illinoinensis) nut shell is an important byproduct of the food processing industry that has not been previously explored as an antioxidant compound. This work aims to study the effect of the extrusion temperature and screw speed on the moisture content, water and oil absorption index, water solubility index, color, phenolic compounds, condensed tannin compounds, and antioxidant activity of pecan nut shell extrudates. Extrusion variables were adjusted using a response surface methodology. Extrusion, performed at 70 °C and 150 rpm, almost doubled the concentration of polyphenols in the non-extruded shell and significantly increased radical scavenging activity. Compounds in extrudates, performed at 70 °C and 150 rpm, were quantified by high-performance liquid chromatography (HPLC) with a diode-array detector (DAD) and identified by liquid chromatography coupled with time-of-flight mass spectrometry (LC-MSD-TOF). Extrusion significantly increased most phenolic acid compounds, including gallic acid, ellagic acid pentose, ellagic acid, dimethyl ellagic acid rhamnoside, and dimethyl ellagic acid. The soluble fiber in extrudates was more than three-fold higher than in the control. Therefore, extrusion at 70 °C and 150 rpm increased the concentration of phenolic compounds, antioxidant activity, and total dietary and soluble fiber. Our findings support the notion that extruded pecan nut shell can be used in clean-label products and improve their nutraceutical value.