Background: The purpose of this study was to investigate the possible effects of ischemic preconditioning (IP) on the second choke zone of extensive perforator flap in a rat model, and whether pedicle selection for IP influenced its efficacy. Methods: A rat perforator flap model, encompassing three vascular territories, was used. In total, 60 rats were divided into one control and two IP groups (primary pedicle, secondary pedicle). On day 7, evaluation of survival area and angiography of the flap were performed. Tissue samples were collected from the second choke zone for histological analyses, western blot, and real-time qRT-PCR. Results: The percentage of flap survival area was greater in both IP groups than in the control group (P < 0.001). There was no significant difference between IP groups (P > 0.05). In both IP groups, the second choke vessels dilated extensively, whereas in the control group, they dilated only slightly or remained unopened. The number of CD31-positive vessels of the second choke zone was increased in IP groups. The vascular diameter was greater in IP groups than in control group. The expression of hypoxia inducible factor-1 alpha and inducible nitric oxide synthase was higher in both IP groups than in control group (P < 0.001), but there was no different between IP groups (P > 0.05). Conclusion: IP has a protective effect on ischemia of skin flaps through effects on the second choke zone. Secondary pedicle IP was as effective as primary pedicle IP on the second choke zone of skin flaps.