At least four non-coplanar anchor nodes (ANs) are required for the time-of-arrival (ToA)-based three-dimensional (3D) positioning to enable unique position estimation. Direct method (DM) and particle filter (PF) algorithms were developed to address the three-anchor ToA-based 3D positioning problem. The proposed DM reduces this problem to the solution of a quadratic equation, exploiting the knowledge about the workspace, to first estimate the x- or z-coordinate, and then the remaining two coordinates. The implemented PF uses 1000 particles to represent the posterior probability density function (PDF) of the AN’s 3D position. The prediction step generates new particles by a resampling procedure. The ToA measurements determine the importance of these particles to enable updating the posterior PDF and estimating the 3D position of the AN. Simulation results corroborate the viability of the developed DM and PF algorithms, in terms of accuracy and computational cost, in the pursuit and circumnavigation scenarios, and even with a horizontally coplanar arrangement of the three ANs. Therefore, it is possible to enable applications requiring real-time positioning, such as unmanned aerial vehicle (UAV) autonomous docking and circling a stationary (or moving) position, without the need for an excessive number of ANs.