Continuous-time (CT) models have shown an improved sample efficiency during learning and enable ODE analysis methods for enhanced interpretability compared to discrete-time (DT) models. Even with numerous recent developments, the multifaceted CT state-space model identification problem remains to be solved in full, considering common experimental aspects such as the presence of external inputs, measurement noise, and latent states. This paper presents a novel estimation method that includes these aspects and that is able to obtain state-of-the-art results on multiple benchmarks where a small fully connected neural network describes the CT dynamics. The novel estimation method called the subspace encoder approach ascertains these results by altering the well-known simulation loss to include short subsections instead, by using an encoder function and a state-derivative normalization term to obtain a computationally feasible and stable optimization problem. This encoder function estimates the initial states of each considered subsection. We prove that the existence of the encoder function has the necessary condition of a Lipschitz continuous state-derivative utilizing established properties of ODEs.