Contact mechanics is a complex and advanced field of engineering, with continuous research dedicated to modeling and examining contact problems in multilayered and multibody systems. Given that fatigue and fracture failures often result from contact loads, precise determination of subsurface stresses is crucial for the design of mechanical components. This study provides an exact analytical solution for the frictionless indentation of a functionally graded (FG) orthotropic layer by a rigid cylindrical punch. The FG orthotropic layer, which rests on a rigid, non-adhesive substrate, is treated as a nonhomogeneous medium with an orthotropic stress–strain relationship. Part of its top surface experiences normal tractions, while the rest remains traction-free. The analysis also incorporates the gravitational force affecting the FG orthotropic layer. Five distinct real orthotropic materials are used, each with individually graded stiffness constants in their principal directions, to define the FG orthotropic behavior of the material. The governing equations are formulated using the singular integral equation method and transformed into algebraic systems via the Gauss–Chebyshev integration technique. A comprehensive parametric study examines how variations in dimensionless punch radius, compressive force, inhomogeneity parameters, and body force influence contact widths, contact pressures, normal and shear stresses, critical load factor, and the initial point of interface separation.