Purpose: To generalize and experimentally validate a new algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a few 2D conebeam‐CT x‐ray projections. Methods and materials: The iterative forward projection matching (IFPM) algorithm finds the set of seed poses that minimizes the sum‐of‐intensity‐difference‐squared (SSD) of computed and experimentally‐acquired auto‐segmented rojections of the seed array. IFPM starts with an initial approximation to the seed configuration, e.g., the pre‐planned seed arrangement and then iteratively refines the 3D seed pose and imaging viewpoint parameters until the SSD converges. We have demonstrated the IFPM method using both synthetic projection images of clinically‐realistic Model‐6711 seed arrangements and measured projections of an in‐house precision‐machined prostate implant phantom that allows the orientations and locations of up to 100 seeds to be set to known values. The phantom was scanned using an Acuity‐digital‐simulator with full 660‐projections. Three‐to‐ten x‐ray projection images were selected from the conebeam‐CT dataset and were pre‐processed to create binary seed‐only images. In addition to comparing the reconstructed to the known seed poses, 2D matching accuracy was quantified comparing the reconstructed seed projection with the measured projection using the dice‐similarity‐coefficient (DSC). The estimated 3D seed positions were also compared with clinically obtained VariSeed‐planning coordinates derived from conebeam‐CT images. Results: For the simulations, the seed reconstruction error was better than 0.4mm/2°. For the phantom experiments, IFPM absolute accuracy was (0.56±0.45)mm for position, while and (2.9±2.8)° and (3.6±4.0)° for polar and azimuthal angles, respectively. The DSC was better than 0.76 in each image‐pair. Conclusions: We have developed a novel algorithm for accurately recovering 3D pose of implanted brachytherapy seeds from as few as 3 projections. IFPM avoids the need to match corresponding seeds in each projection and accommodates incomplete data, overlapping seed clusters, and highly‐migrated seeds. Supported by Varian Medical Systems.