Loach protein hydrolysates (LPH) prepared by papain digestion were fractionated into four fractions, LPH-I (MW > 10 kDa), LPH-II (MW = 5-10 kDa), LPH-III (MW = 3-5 kDa), LPH-IV (MW < 3 kDa), and the in vitro antioxidant and antiproliferative (anticancer) activities of all fractions were determined. LPH-IV showed the lowest IC(50) value (16.9 ± 0.21 mg/mL) for hydroxyl radical scavenging activity and the highest oxygen radical scavenging capacity (ORAC) value (reaching 215 ± 5.9 mM Trolox/100 g loach peptide when the concentration was 60 μg/mL). Compared with other fractions, LPH-IV also exhibited stronger antiproliferative activity for human liver (HepG2), breast (MCF-7), and colon (Caco-2) cancer cell lines in a dose-dependent manner. When the protein concentration was 40 mg/mL, the HepG2 and MCF-7 cell proliferation of LPH-IV reached 7 and 4%, respectively, with no significant difference from those of LPH (8 and 7%, p > 0.05), with significantly less growth than those of LPH-I, LPH-II, and LPH-III, respectively (p < 0.05). The Caco-2 colon cell proliferation of LPH-IV was 12.8- and 8.7-fold smaller than those of LPH-I and LPH-II, respectively (p < 0.05). All of the fractions had a greater ability to inhibit Caco-2 colon cancer cell proliferation than to inhibit HepG2 liver cancer and MCF-7 breast cancer cell proliferation. The ORAC values of most of the fractions correlated (R(2) > 0.86, p < 0.01) with the antiproliferative activity of the three cancer cell lines, suggesting that higher antioxidant activity leads to better antiproliferative activity. However, further mechanistic and human clinical studies of the anticancer activity of loach protein hydrolysate fractions are needed.