This paper realises the Khovanov homology of a link in $ S^3$ as a Lagrangian Floer cohomology group, establishing a conjecture of Seidel and the second author. The starting point is the previously established formality theorem for the symplectic arc algebra over a field $ \mathbf {k}$ of characteristic zero. Here we prove the symplectic cup and cap bimodules, which relate different symplectic arc algebras, are themselves formal over $ \mathbf {k}$, and we construct a long exact triangle for symplectic Khovanov cohomology. We then prove the symplectic and combinatorial arc algebras are isomorphic over $ \mathbb{Z}$ in a manner compatible with the cup bimodules. It follows that Khovanov cohomology and symplectic Khovanov cohomology co-incide in characteristic zero.