Background: Australian patients with chronic kidney disease (CKD) are routinely managed in general practices with multiple medications. However, no nationally representative study has evaluated the quality of prescribing in these patients. The objective of this study was to examine the quality of prescribing in patients with CKD using nationally representative primary care data obtained from the NPS MedicineWise’s dataset, MedicineInsight. Methods: A cross-sectional analysis of general practice data for patients aged 18 years or older with CKD was performed from 1 February 2016 to 1 June 2016. The study examined the proportion of patients with CKD who met a set of 16 published indicators in two categories: (1) potentially appropriate prescribing of antihypertensives, renin-angiotensin system (RAS) inhibitors, phosphate binders, and statins; and (2) potentially inappropriate prescribing of nephrotoxic medications, such as non-steroidal anti-inflammatory drugs (NSAIDs), at least two RAS inhibitors, triple therapy (an NSAID, a RAS inhibitor and a diuretic), high-dose digoxin, and metformin. The proportion of patients meeting each quality indicator was stratified using clinical and demographic characteristics. Results: A total of 44,259 patients (24,165 (54.6%) female; 25,562 (57.8%) estimated glomerular filtration (eGFR) 45–59 mL/1.73 m2) with CKD stages 3–5 were included. Nearly one-third of patients had diabetes and were more likely to have their blood pressure and albumin-to-creatinine ratio monitored than those without diabetes. Potentially appropriate prescribing of antihypertensives was achieved in 79.9% of hypertensive patients with CKD stages 4–5. The prescribing indicators for RAS inhibitors in patients with microalbuminuria and diabetes and in patients with macroalbuminuria were achieved in 69.9% and 62.3% of patients, respectively. Only 40.8% of patients with CKD and aged between 50 and 65 years were prescribed statin therapy. The prescribing of a RAS inhibitor plus a diuretic was less commonly achieved, with the indicator met in 20.6% for patients with microalbuminuria and diabetes and 20.4% for patients with macroalbuminuria. Potentially inappropriate prescribing of NSAIDs, metformin, and at least two RAS inhibitors were apparent in 14.3%, 14.1%, and 7.6%, respectively. Potentially inappropriate prescribing tended to be more likely in patients aged ≥65 years, living in regional or remote areas, or with socio-economic indexes for areas (SEIFA) score ≤ 3. Conclusions: We identified areas for possible improvement in the prescribing of RAS inhibitors and statins, as well as deprescribing of NSAIDs and metformin in Australian general practice patients with CKD.