Background: An invasive phlebological treatment is still not free from complications such as thrombosis. As in other surgical populations, not only the treatment modality, but also patient condition-related venous thromboembolism (VTE) risk factors matter. The current protocols used in varicose vein surgery centers are based mostly on individual risk assessment as well as on an implementation and extrapolation of general surgery VTE prophylaxis guidelines. In the presented study, the efficacy of routine VTE pharmacological thromboprophylaxis in patients undergoing saphenous varicose vein surgery was prospectively evaluated. In the result assessment, VTE risk factor evaluation and Caprini score results were included; however, due to the limited size of the projected study group, as well as expected limited deep vein thrombosis (DVT) prevalence in this clinical scenario, it was not possible to perform the validation of the Caprini model efficacy in the projected study model. Methods: In the study, 141 patients undergoing saphenous vein stripping and miniphlebectomy in spinal anesthesia were included. In all of the patients, VTE risk factors (including Caprini score evaluation) were assessed, and the routine thromboprophylaxis with enoxaparin 40 mg for 10 days was used. The venous ultrasounds were undertaken before the surgery and on the 10th and 30th day after surgery. The study endpoint was the presence of symptomatic or asymptomatic DVT confirmed in the imaging study. The study safety endpoint was major bleeding occurrence intraoperatively or within 30 days after surgery. Results: The presence of a postoperative DVT was diagnosed in five cases (3.5%) In all of these cases, only distal DVT was confirmed. Despite extensive saphenous varicose vein surgery with stripping and miniphlebectomy performed in nontumescent but spinal anesthesia, no proximal lower leg episode was diagnosed. Three out of five DVT cases were diagnosed on day 10 postoperative control, while a further two were confirmed in the ultrasound examination performed 30 days after procedure. No clinically documented pulmonaly embolism (PE) as well as no bleeding episodes were noticed. Among the factors related to the statistically significant higher DVT occurrence, the results of the Caprini score were identified with odds ratio (OR) = 2.04 (95% CI = (0.998; 4.18)). Another factor that became statistically significant in terms of the higher postoperative DVT prevalence was the reported Venous Clinical Severity Score (VCSS) results (OR = 1.98; 95% CI (1.19; 3.26)). In the multiple logistic regression analysis, the patient age (OR = 0.86; 95% CI (0.75–0.99)), Caprini score evaluation results (OR = 4.04; 95% CI (1.26–12.9)) and VCSS results (OR = 2.4; 95% CI (1.23–4.7)) were of statistical significance as predictors for postoperative DVT occurrence, with a p value of 0.029 for age, and p = 0.017 and p = 0.009 for Caprini score results and VCSS results, respectively. Due to the confirmed limited number of the DVT events in our study cohort, as well as the descriptive and explorative nature of the achieved results, the final clinical potential and significance of the identified parameters, including Caprini score rate and VCSS rate, should be interpreted with caution and studied in the further trials in these clinical settings. Conclusion: All the patients undergoing varicose vein surgery should undergo VTE risk evaluation based on the individual assessment. In VTE risk evaluation, patient and surgical procedure characteristics based on the factors included into the Caprini score but also on specific chronic venous disease-related factors should be taken into consideration. Further studies are needed to propose an objective and validated VTE risk assessment model, as well as a validated antithrombotic prophylaxis protocol in this particular patient group.