The banana passion fruit (Passiflora tripartita Breiter, Passifloraceae) known as “tumbo” is very appreciated in tropical and subtropical countries of South America. Methanolic extracts from peel and the fruit juice of P. tripartita growing in Chile were analyzed for antioxidant capacity as well as for flavonoid and phenolic content. A chromatographic method was developed for the rapid identification of the main phenolics in the samples by HPLC-DAD and HPLC-MS. The fast fingerprint analysis allowed the detection of eighteen flavonoid C-glycosides and four flavonoid O-glycoside derivatives which were characterized by UV spectra and ESI-MS-MS analysis. Several of the C-glycosides detected are structurally related to the orientin derivative 4′-methoxy-luteolin-8-C-(6″acetyl)-b-D-glucopyranoside (31), fully elucidated by spectroscopic methods. The antioxidant derivative 31 along with schaftoside, vicenin II, orientin and vitexin were isolated from the fruit extract by high-speed countercurrent chromatography (HSCCC). A suitable method for the preparative isolation of flavonol C-glycosides from “tumbo” extracts by HSCCC is reported. The pulp of the fruits showed good antioxidant capacity (12.89 ± 0.02 mg/mL in the DPPH assay). The peel presented the highest content of flavonoids (56.03 ± 4.34 mg quercetin/100 g dry weight) which is related to the highest antioxidant power (10.41 ± 0.01 mg/mL in the DPPH assay).