Thrombus perviousness is strongly associated with functional outcome and intravenous alteplase treatment success in patients with acute ischemic stroke. Accuracy of thrombus attenuation increase (TAI) assessment may be compromised by a heterogeneous thrombus composition and interobserver variations of currently used manual measurements. We hypothesized that TAI is more strongly associated with clinical outcomes when evaluated on the entire thrombus. In 195 patients, five TAI measures were performed: one manual by placing three regions of interest (TAImanual) and four automated ones assessing densities from the entire thrombus. The automated TAI measures were calculated by comparing quartiles; Q1, Q2, and Q3 of the non-contrast and contrast enhanced thrombus density distribution and using the lag of the maximum of the cross correlations (MCC). Associations with functional outcome (mRS at 90 days) were assessed with univariate and multivariable analyses. All entire TAI measures were significantly associated with functional outcome with odd ratios (OR) of 1.63(95 %CI:1.19–2.25, p = 0.003) for Q1, 1.56(95 %CI:1.16–2.10, p = 0.003) for Q2, 1.24(95 %CI:1.00–1.54, p = 0.045) for Q3, and 1.70(95 %CI:1.24–2.34, p = 0.001) for MCC per 10 HU increase in univariate models. TAImanual was not significantly associated with functional outcome (p = 0.055). In the multivariable logistic regression models including age, NIHSS, and recanalization, only TAI measures derived from the entire thrombus were independently associated with favorable outcome; OR of 1.64(95 %CI:1.01–2.66, p = 0.048) for Q2 and 1.82(1.13–2.95, p = 0.014) for MCC per 10 HU increase of thrombus attenuation. The novel perviousness measures of the entire thrombus are more strongly associated with functional outcome than the traditional manual perviousness assessments.