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Root System Architecture (RSA) plays an important role in the agronomic performance of a crop. Incorporation of these root traits in breeding program is hampered by the complexity in accessing the roots and its phenotyping. Lack of high throughput root phenotyping platforms for sugarcane is one of the major constraints in sugarcane root studies. In the present study an attempt was made to develop high throughput sugarcane root phenotyping pipeline comprising of a low cost plant cultivation platform and customized root image acquisition platform and image analyses using already available automated software. PVC tube system of specified dimension were used for plant growth and customized optical correction tank were used for imaging RSA. The acquired root images were fed into automated software GIAroots and about twenty quantitative root phenotype data were extracted and analysed. The working of the whole pipeline from plant growth to image analyses is demonstrated through comparative root phenotyping under drought using five genotypes of sugarcane wild relative Erianthus arundinaceus and three commercial sugarcane varieties.The relationships between the different root variables and genotypes in PCA biplots indicated high correlation among the different root traits. The study shows the low cost high throughput image based root phenotyping pipeline can be used to extract quantifiable root traits and analysed within a short span of time.