Despite being studied extensively, there are still many knowledge gaps in milk fever prevention and it is still a prevalent disease. Various interventions have been used in its prevention; however, none has proven to be entirely effective. The study aimed to assess the effectiveness of high dose vitamin D3 parenteral (intramuscularly) administration and the mechanism of its action by studying blood minerals and biochemical bone markers. Further, we assessed the potential of biochemical bone markers, measured in the close-up dry period, as predictors of clinical milk fever after calving. The study was conducted on 56 high yielding, clinically healthy dairy cows, before their 4th or higher lactation. They were divided into three groups based on season (summer and winter) and administration (vitamin D). The winter group was considered as the control group. Cows (n = 13) were parenterally administered a single dose of 10 million IU of vitamin D3 (DUPHAFRAL® D3) ranging between 10 and 2 days before calving (median = 3 days). Each cow was blood sampled once during four sampling period ranges: ~1 month before calving, 10 to 2 days before calving, 12–48 h after calving and 10–20 days after calving. The samples were analyzed for blood minerals, bone specific alkaline phosphatase (bALP) and C-terminal telopeptide of type I collagen (CTx), alkaline phosphatase, and estradiol. Values were compared between samplings and groups. A receiver operating characteristic (ROC) analysis and logistic regression were used to assess the diagnostic accuracy of biochemical bone markers in predicting milk fever. In this study high dose vitamin D3 supplementation did not statistically reduced the incidence of milk fever (milk fever incidences were 15.4, 39.1, and 25% in the vitamin D, winter and summer groups, respectively). A significant effect of vitamin D3 administration on blood minerals or biochemical bone markers was not found at any sampling. We found that the use of biochemical bone markers in the close-up dry period to predict clinical milk fever was applicable only in the winter (housed) group. The area under the curve (AUC) for bALP was 0.804 and 0.846 for CTx using ROC analysis. The bALP curve had the best ratio at the cut-off point 13.85 U/L with 90% sensitivity and 64.3% specificity. While CTx had the ratio of 90% sensitivity and 78.6% specificity at the cut-off point 0.149 ng/mL. Close-up dry dairy cows with CTx ≥0.121 ng/mL had a 3.8 times higher chance of succumbing to milk fever. We were unable to prove that high dose vitamin D3 parenteral administration is a viable technique for milk fever prevention. Biochemical bone markers are a promising tool for predicting milk fever; however, further studies are needed to confirm their clinical use.