Deprescribing is a notable approach to improve medication management, but few healthcare systems recognize it. To introduce a new practice, it is important to examine the factors influencing the provision of a new or elaborate cognitive service within the desired setting. This study explores the perceived barriers and facilitators of deprescribing by primary healthcare providers, and identifies the factors associated with a willingness to suggest deprescribing. A cross-sectional survey was conducted (in Croatia, between October 2021 and January 2022) using a validated comprehensive healthcare providers’ opinions, preferences, and attitudes towards deprescribing (CHOPPED) questionnaire. A total of 419 pharmacists and 124 physicians participated. Participants showed a high willingness to deprescribe, with significantly higher scores in physicians than in pharmacists (5.00 (interquartile range—IQR 5–5) vs. 4.00 (IQR 4–5), p < 0.001). Pharmacists had significantly higher scores in seven out of ten factors (knowledge, awareness, collaboration facilitators, competencies facilitators, healthcare system facilitators, collaboration barriers, competencies barriers) while in the remaining three factors (patient facilitators, patient and healthcare system barriers) there was no difference in scores. The strongest positive correlation with willingness to suggest deprescribing was found with the collaboration and healthcare system facilitators factors for pharmacists (G = 0.331, p < 0.001, and G = 0.309, p < 0.001, respectively), and with knowledge, awareness, and patient facilitators factors for physicians (G = 0.446, p = 0.001; G = 0.771, p < 0.001; and G = 0.259, p = 0.043, respectively). Primary healthcare providers are willing to suggest deprescribing but face different barriers and facilitators. For pharmacists, the most important facilitators were extrinsic, while for physicians they were more intrinsic and patient related. The stated results provide target areas which one could focus upon to help to engage healthcare providers in deprescribing.