Three C90 fractions were isolated by multi‐step HPLC from fullerene soot obtained from direct current (DC) arc discharge of undoped graphite rods. C90 of each fraction was chlorinated with VCl4 or SbCl5 in ampoules at 290–310 °C, affording a series of C90Cln compounds. Single‐crystal X‐ray crystallography with the use of synchrotron radiation resulted in structure elucidation of seven C90Cln compounds containing six different isolated pentagon rule (IPR) C90 cages (the number of the C90 isomer is given in the parentheses): C90(46)Cl32 (I), C90(34)Cl32 (II), C90(35)Cl24 (III), and C90(35)Cl28 (IV), C90(32)Cl24 (V as co‐crystals with III), co‐crystals of C90(30)Cl22 and C90(28)Cl24 (VI), and C90(28)Cl24 (VII). Cage connectivities of C90 isomers 35 and 28 have been crystallographically confirmed for the first time. The chlorination patterns of the C90Cln molecules are discussed in terms of the formation of isolated aromatic systems and isolated CC double bonds on the fullerene cage. The distribution of six C90 isomers in three HPLC fractions is compared with data from the literature.