Abstract Purpose The crystalline lens undergoes morphological and functional changes with age and may also play a role in eye emmetropisation. Both the geometry and the gradient index of refraction (GRIN) distribution contribute to the lens optical properties. We studied the lens GRIN in the guinea pig, a common animal model to study myopia. Methods Lenses were extracted from guinea pigs ( Cavia porcellus) at 18 days of age ( n = 4, three monolaterally treated with negative lenses and one untreated) and 39 days of age ( n = 4, all untreated). Treated eyes were myopic (−2.07 D on average) and untreated eyes hyperopic (+3.3 D), as revealed using streak retinoscopy in the live cyclopeged animals. A custom 3D spectral domain optical coherence tomography (OCT) system (λ = 840 nm, Δλ = 50 nm) was used to image the enucleated crystalline lens at two orientations. Custom algorithms were used to estimate the lens shape and GRIN was modelled with four variables that were reconstructed using the OCT data and a minimisation algorithm. Ray tracing was used to calculate the optical power and spherical aberration assuming a homogeneous refractive index or the estimated GRIN. Results Guinea pig lenses exhibited nearly parabolic GRIN profiles. When comparing the two age groups (18‐ and 39 day‐old) there was a significant increase in the central thickness (from 3.61 to 3.74 mm), and in the refractive index of the surface (from 1.362 to 1.366) and the nucleus (from 1.443 to 1.454). The presence of GRIN shifted the spherical aberration (−4.1 µm on average) of the lens towards negative values. Conclusions The guinea pig lens exhibits a GRIN profile with surface and nucleus refractive indices that increase slightly during the first weeks of life. GRIN plays a major role in the lens optical properties and should be incorporated into computational guinea pig eye models to study emmetropisation, myopia development and ageing.