Quantification of infarct size is a very useful index to assess models of focal cerebral ischemia and effects of new therapies. Currently-used image analysis systems to carry out this task usually involve dedicated and expensive equipment. We present a low-cost and simple method to perform the image acquisition and analysis. Twelve Wistar rats were subject to focal cerebral ischemia and scarified 24 h after the insult. 2,3,5-triphenyl tetrazolium chloride (TTC) stain was used as a conventional method to differentiate ischemic damage from healthy brain tissue. Digital images were captured from the stained coronal sections using a flatbed color scanner and analyzed with a commercial image processing software. To evaluate the accuracy and reproducibility of this method, the data obtained with the current procedure was correlated with those from a dedicated standard image analysis system and intra-observor correlation coefficient was estimated. Also the sensitivity of this method in quantification of infarct volume was tested in two different experimental settings. There was close correlation in the outcome of infarct size measurement between the current method and the standard system (r = 0.93, p < 0.001). A high agreement of measurement of the percentage of infarct volume between two different examiners with the same source of samples (r = 0.98, p < 0.001). We demonstrated that this method was sensitive in detection of difference of infarct sizes when placebo-treated animals (n = 6) were compared to the group treated with a neuroprotective agent (n = 6). Our data demonstrated that ischemic lesion of focal cerebral ischemia in rat can be accurately and reproducibly quantified using this method. The low-cost and simplicity of this method may facilitate the application in determination of ischemic damage.