This study is concerned with the removal performance of the antibiotic ciprofloxacin (CIP) from synthetic solutions by electrocoagulation (EC), as well as the toxic effects of treated CIP solutions. A response surface analysis (RSA) was applied to search optimal operational parameter values of the pH of solution, electrical current density (ECD), and electrolysis time (ET). The EC efficiency was evaluated by determining the total organic carbon (TOC) and CIP concentration performed by high-performance liquid chromatography. Although the best EC efficiency was attained at pH = 8, ECD = 22.2 A m−2, and ET = 75 min, toxicity and antibacterial tests were performed using Artemia salina cysts and Staphylococcus aureus and Escherichia coli microorganisms in a wide ET range and other pH and ECD values. Increasing optimal pH value (9), along with reducing optimal ECD value (18 A m−2) and regarding low ET values, similar results for the removal of CIP (98%) and TOC (87%) were also attained. Toxicity variation was observed during EC process in synthetic solutions with the lowest antibacterial effects due to CIP and recalcitrant compound residues after 40 min of ET. These results clearly showed that the EC process presents a promising alternative method for the treatment of wastewaters containing high CIP concentrations.