The physicochemical characteristics and functional properties of pumpkin (Cucurbita maxima D. var. Cabello de Ángel) pectin obtained by cavitation facilitated extraction from pumpkin pulp have been evaluated and compared with commercial citrus and apple pectins. C. maxima pectin had an Mw value of 90 kDa and a high degree (72%) of esterification. The cytoprotective and antioxidant effects of citrus, apple and pumpkin pectin samples with different concentrations were studied in vitro in cell lines HT-29 (human colon adenocarcinoma) and MDCK1 (canine kidney epithelium). All pectin samples exhibited cytoprotective effect in HT-29 and MDCK1 cells after incubation with toxic concentrations of cadmium and mercury for 4 h. Pumpkin pectin increased the proliferation of cadmium-treated MDCK1 cells by 210%. The studied pectins also inhibited oxidative stress induced by 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH) in cell cultures, as determined by measuring the production of intracellular reactive species using dihydrochlorofluorescein diacetate (DCFH-DA). Pectin from pumpkin pomace had the highest (p < 0.05) protective effect against reactive oxygen species generation in MDCK1 cells induced by AAPH. Distinctive features of pumpkin pectin were highly branched RG-I regions, the presence of RG-II regions and the highest galacturonic acid content among the studied samples of pectins. This correlates with a considerable protective effect of C. maxima pectin against oxidative stress and cytotoxicity induced by heavy metal ions. Thus, C. maxima pectin can be considered as a source of new functional foods of agricultural origin.