Three-dimensional heteroatom-doped graphene presents a state-of-the-art approach for effective remediation of pharmaceutical wastewater on account of its distinguished adsorption and physicochemical attributes. Amitriptyline is an emerging tricyclic antidepressant pollutant posing severe risks to living habitats through water supply and food chain. With ultra-large surface area and plentiful chemical functional groups, graphene oxide is a favorable adsorbent for decontaminating polluted water. Herein, a new boron-doped graphene oxide composite reinforced with carboxymethyl cellulose was successfully developed via solution-based synthesis. Characterization study revealed that the adsorbent was formed by graphene sheets intertwined into a porous network and engrafted with 13.37 at% of boron. The adsorbent has a zero charge at pH 6 and contained various chemical functional groups favoring the attachment of amitriptyline. It was also found that a mere 10 mg of adsorbent was able to achieve relatively high amitriptyline removal (89.31%) at 50 ppm solution concentration and 30 °C. The amitriptyline adsorption attained equilibrium within 60 min across solution concentrations ranging from 10 to 300 ppm. The kinetic and equilibrium of amitriptyline adsorption were well correlated to the pseudo-second-order and Langmuir models, respectively, portraying the highest Langmuir adsorption capacity of 737.4 mg/g. Notably, the predominant mechanism was chemisorption assisted by physisorption that contributed to the outstanding removal of amitriptyline. The saturated adsorbent was sufficiently regenerated using ethanol eluent. The results highlighted the impressive performance of the as-synthesized boron-doped adsorbent in treating amitriptyline-containing waste effluent.