Determination of strontium ions (Sr2+) is crucial with regard to human health and environmental protection. In this work, an electrochemical aptasensor was designed using carboxylated graphene oxide (CGO)-modified carbon paste electrode (CGO/CPE) for ultrasensitive determination of Sr2+ ions. The electrochemical determination was accomplished with employing the constructed G-quadruplex (G4) aptamer at the surface of aptasensor in presence of carmoisine (CA) as an electrochemical label. Moreover, NH2-functionalized aptamer was immobilized onto CGO/CPE via carboxylic group. Hence, differential pulse voltammetry was applied for detection of any possible signal changes of CA on the aptasensor surface. The reduction peak currents of CA in the absence and presence of Sr2+ in solution were different and this difference was linearly dependent to the concentration of Sr2+ in solution. The analytical results revealed that our novel aptasensor showed two appropriate linear ranges (0.1–8.0 pM and 3.0–20.0 nM) versus to Sr2+ ion concentrations with the limit of detection of 0.06 pM (S/N = 3). Excellent stability, selectivity and reproducibility were achieved with this new electrochemical aptasensor. Additionally, the aptasensor showed good achievements in analysis of Sr2+ in aqueous and urine real samples, which making this proposed method a promising candidate for electrochemical detection of Sr2+ in real samples.