•Surgical planning of pediatric craniovertebral anomalies is requires multiplanar CT reconstructions.•Screw trajectories can be planned in 4 steps using an open-source DICOM manipulation software.•This method gives more anatomical information compared to studying conventional PACS images. Computed tomography (CT) images provided by the radiology department may be inadequate for planning screws for rigid craniovertebral junction (CVJ) instrumentation. Although many recommend using multiplanar reconstruction (MPR) in line with screw trajectories, this is not always available to all surgeons. The current study aims to present a step-by-step workflow for preoperative planning for pediatric CVJ anomalies. Twenty-five consecutive children (<12 years) were operated for atlantoaxial instability between 2014 and 2019. Preoperative CT angiograms were transferred to an open-source software called Horos™. The surgeon manipulated images in this viewing software to determine an idealized path of screws. Three-dimensional volume rendering of the pathoanatomy was generated, and anomalies were noted. The surgeon compared the anatomical data obtained using Horos™ with that from the original imaging platform and graded it as; Grade A (substantial new information), Grade B (confirmatory with improved visualization and understanding), Grade C (no added information). The surgeon then executed the surgical plan determined using Horos™. Surgeries performed were occipitocervical (n = 18, 72%) and atlantoaxial fixation (n = 7, 28%) at a mean age of 7.2 years, with 72% of etiologies being congenital or dysplasias. In 18 (72%) patients, the surgeon noted substantial new information (Grade A) about CVJ anomalies on Horos™ compared to original imaging platform. Concerning planning for fixation anchors, the surgeon graded A in all patients (100%). In 4 (16%) patients, the surgery could not be executed precisely as planned. There were three (12%) complications; VA injury (n = 1), neurological worsening (n = 1), and loss of fixation (n = 1). In our experience, surgeon-directed imaging manipulation gives more anatomical information compared to studying original imaging planes and should be incorporated in the surgeon's preoperative workup. When image reformatting options are limited, open-source software like Horos™ may offer advantages.