The influence of conventional and novel extraction technologies on the structure-prebiotic activity relationship of fucoidan extracts was investigated. Fucoidan extracted from conventional chemical (Fuc-CCE), microwave-assisted (Fuc-MAE), ultrasound-assisted (Fuc-UAE) and enzyme-assisted (Fuc-EAE) extractions were characterized and investigated for in vitro prebiotic activity. Fuc-CCE had significantly higher extract yield when compared to Fuc-MAE, Fuc-UAE, and Fuc-EAE. However, there were no significant differences in fucose and galactose contents of the extracts. Sulphate levels of Fuc-MAE and Fuc-CCE were significantly higher than those of Fuc-UAE and Fuc-EAE. Also, Fuc-MAE had significantly lower average molecular weight and higher dispersity index compared to the other extracts. Fucoidan-supplemented MRS broth from all four methods significantly (p < 0.05) increased growth rates of Lactobacillus delbruecki ssp bulgaricus compared to the un-supplemented medium. However, there was no significant difference in the growth rates of the extracts. For the L. casei strain, there was no significant difference between the supplemented and un-supplemented media. However, Fuc-MAE-supplemented media resulted in a 24.5% increase in growth rate, at 0.5% w/v concentration, compared to the un-supplemented medium. The growth rates of fucoidan extracts were comparable to that of the commercial prebiotic, inulin, thus strengthening the in vitro prebiotic claim for the fucoidan extracts. Overall, the results indicated that Fuc-MAE had better physicochemical characteristics (fucose and galactose, sulphate, molecular weight and dispersity index), but had no significant advantage over the other extracts based on in vitro prebiotic activity.