Background Potentially inappropriately prescribed medications (PIPMs) among patients with chronic kidney disease (CKD) may vary among clinical settings. Rates of PIPM are unknown among Medicare-enrolled Medication Therapy Management (MTM) eligible patients. Objectives Determine prevalence of PIPM among patients with CKD and evaluate characteristics of patients and providers associated with PIPM. Design An observational cross-sectional investigation of a Medicare insurance plan for the year 2018. Patients Medicare-enrolled MTM eligible patients with stage 3–5 CKD. Main Measures PIPM was identified utilizing a tertiary database. Logistic regression assessed relationship between patient characteristics and PIPM. Key Results Investigation included 3624 CKD patients: 2856 (79%), 548 (15%), and 220 (6%) patients with stage 3, 4, and 5 CKD, respectively. Among patients with stage 3, stage 4, and stage 5 CKD, 618, 430, and 151 were with at least one PIPM, respectively. Logistic regression revealed patients with stage 4 or 5 CKD had 7–14 times the odds of having a PIPM in comparison to patients with stage 3 disease (p < 0.001). Regression also found PIPM was associated with increasing number of years qualified for MTM (odds ratio (OR) 1.46–1.74, p ≤ 0.005), female gender (OR 1.25, p = 0.008), and increasing polypharmacy (OR 1.30–1.57, p ≤ 0.01). Approximately 14% of all medications (2879/21093) were considered PIPM. Majority of PIPMs (62%) were prescribed by physician primary care providers (PCPs). Medications with the greatest percentage of PIPM were spironolactone, canagliflozin, sitagliptin, levetiracetam, alendronate, pregabalin, pravastatin, fenofibrate, metformin, gabapentin, famotidine, celecoxib, naproxen, meloxicam, rosuvastatin, diclofenac, and ibuprofen. Conclusion Over one-third of Medicare MTM eligible patients with CKD presented with at least one PIPM. Worsening renal function, length of MTM eligibility, female gender, and polypharmacy were associated with having PIPM. Majority of PIPMs were prescribed by PCPs. Clinical decision support tools may be considered to potentially reduce PIPM among Medicare MTM–enrolled patients with CKD.