Recently it was demonstrated that Sr intercalation provides a new route to induce superconductivity in the topological insulator Bi2Se3. Topological superconductors are predicted to be unconventional with an odd-parity pairing symmetry. An adequate probe to test for unconventional superconductivity is the upper critical field, Bc2. For a standard BCS layered superconductor Bc2 shows an anisotropy when the magnetic field is applied parallel and perpendicular to the layers, but is isotropic when the field is rotated in the plane of the layers. Here we report measurements of the upper critical field of superconducting SrxBi2Se3 crystals (Tc = 3.0 K). Surprisingly, field-angle dependent magnetotransport measurements reveal a large anisotropy of Bc2 when the magnet field is rotated in the basal plane. The large two-fold anisotropy, while six-fold is anticipated, cannot be explained with the Ginzburg-Landau anisotropic effective mass model or flux flow induced by the Lorentz force. The rotational symmetry breaking of Bc2 indicates unconventional superconductivity with odd-parity spin-triplet Cooper pairs (Δ4-pairing) recently proposed for rhombohedral topological superconductors, or might have a structural nature, such as self-organized stripe ordering of Sr atoms.