An effective and reproducible micropropagation protocol was developed for Centratherum punctatum Cass. Successful in vitro initiation of callus and subsequent plant regeneration were obtained on nodal explants cultured on MS medium supplemented with plant growth regulators (PGRs). The maximum frequency of callus formation (98.3%) was noted on MS containing 4.0 mg/L 6-Benzylaminopurine (BAP) and 3.5 mg/L Kinetin with a maximum callus weight of 2.02 g. The best shoot induction frequency (100%) with an average of 30.2 shoots per explant was achieved when 4.5 mg/L BAP and 4.0 mg/L Kinetin were added to the MS. The same PGR combination resulted in the best callus-mediated shoot formation (8.3 shoots/callus mass). The highest rhizogenic response (95.3%) with an average 26.1 roots per shoot and root length of 6.2 cm was obtained with 1.0 mg/L Indole-3-acetic acid (IAA)-supplemented MS medium. The gas chromatography–mass spectrometry (GC-MS) technique was applied in the present study to analyze the methanolic extracts of the leaf, callus, and root of regenerated C. punctatum shoots to detect the different phytochemical constituents. The leaf extract of the regenerated C. punctatum showed 37 phytocompounds; some important bioactive compounds were the Phytol,1,6-Octadien 3,5-Dimethyl-Cis, 4,8-Dimethylnona-3,8-dien-2-one, 2,6-Octadiene, Stigmasterol, Chondrillasterol, Lanosteryl acetate, etc. In the callus, the extract had a total of 57 phytocompounds; among them, the Stigmasterol, Guanosine, and Tri-decanoic acid were the major ones. In the root extract, the GC-MS revealed a low number of 23 phytocompounds, the important compounds of which were Stigmasterol, Trimethylsilyl (TMS) derivative, Chrysantenyl 2-methuylbutanoate, 4-tert-Butoxybutan-1-ol, etc. The order in terms of numbers of phytocompounds present in tissue sources are callus > leaf > root.