diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.js b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.js
index 4540954..84f65a0 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.js
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.js
@@ -56,25 +56,40 @@
 	},
 
 	get_items: function(frm) {
-		let fields = [{
-			label: 'Warehouse', fieldname: 'warehouse', fieldtype: 'Link', options: 'Warehouse', reqd: 1,
-			"get_query": function() {
-				return {
-					"filters": {
-						"company": frm.doc.company,
-					}
-				};
+		let fields = [
+			{
+				label: 'Warehouse',
+				fieldname: 'warehouse',
+				fieldtype: 'Link',
+				options: 'Warehouse',
+				reqd: 1,
+				"get_query": function() {
+					return {
+						"filters": {
+							"company": frm.doc.company,
+						}
+					};
+				}
+			},
+			{
+				label: "Item Code",
+				fieldname: "item_code",
+				fieldtype: "Link",
+				options: "Item",
+				"get_query": function() {
+					return {
+						"filters": {
+							"disabled": 0,
+						}
+					};
+				}
+			},
+			{
+				label: __("Ignore Empty Stock"),
+				fieldname: "ignore_empty_stock",
+				fieldtype: "Check"
 			}
-		}, {
-			label: "Item Code", fieldname: "item_code", fieldtype: "Link", options: "Item",
-			"get_query": function() {
-				return {
-					"filters": {
-						"disabled": 0,
-					}
-				};
-			}
-		}];
+		];
 
 		frappe.prompt(fields, function(data) {
 			frappe.call({
@@ -84,22 +99,21 @@
 					posting_date: frm.doc.posting_date,
 					posting_time: frm.doc.posting_time,
 					company: frm.doc.company,
-					item_code: data.item_code
+					item_code: data.item_code,
+					ignore_empty_stock: data.ignore_empty_stock
 				},
 				callback: function(r) {
+					if (r.exc || !r.message || !r.message.length) return;
+
 					frm.clear_table("items");
-					for (var i=0; i<r.message.length; i++) {
-						var d = frm.add_child("items");
-						$.extend(d, r.message[i]);
 
-						if (!d.qty) {
-							d.qty = 0;
-						}
+					r.message.forEach((row) => {
+						let item = frm.add_child("items");
+						$.extend(item, row);
 
-						if (!d.valuation_rate) {
-							d.valuation_rate = 0;
-						}
-					}
+						item.qty = item.qty || 0;
+						item.valuation_rate = item.valuation_rate || 0;
+					});
 					frm.refresh_field("items");
 				}
 			});
diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 9875491..0bae7cf 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -483,7 +483,8 @@
 			self._cancel()
 
 @frappe.whitelist()
-def get_items(warehouse, posting_date, posting_time, company, item_code=None):
+def get_items(warehouse, posting_date, posting_time, company, item_code=None, ignore_empty_stock=False):
+	ignore_empty_stock = cint(ignore_empty_stock)
 	items = [frappe._dict({
 		'item_code': item_code,
 		'warehouse': warehouse
@@ -497,18 +498,24 @@
 
 	for d in items:
 		if d.item_code in itemwise_batch_data:
-			stock_bal = get_stock_balance(d.item_code, d.warehouse,
-				posting_date, posting_time, with_valuation_rate=True)
+			valuation_rate = get_stock_balance(d.item_code, d.warehouse,
+				posting_date, posting_time, with_valuation_rate=True)[1]
 
 			for row in itemwise_batch_data.get(d.item_code):
-				args = get_item_data(row, row.qty, stock_bal[1])
+				if ignore_empty_stock and not row.qty:
+					continue
+
+				args = get_item_data(row, row.qty, valuation_rate)
 				res.append(args)
 		else:
 			stock_bal = get_stock_balance(d.item_code, d.warehouse, posting_date, posting_time,
 				with_valuation_rate=True , with_serial_no=cint(d.has_serial_no))
+			qty, valuation_rate, serial_no = stock_bal[0], stock_bal[1], stock_bal[2] if cint(d.has_serial_no) else ''
 
-			args = get_item_data(d, stock_bal[0], stock_bal[1],
-				stock_bal[2] if cint(d.has_serial_no) else '')
+			if ignore_empty_stock and not stock_bal[0]:
+					continue
+
+			args = get_item_data(d, qty, valuation_rate, serial_no)
 
 			res.append(args)
 
@@ -516,24 +523,44 @@
 
 def get_items_for_stock_reco(warehouse, company):
 	lft, rgt = frappe.db.get_value("Warehouse", warehouse, ["lft", "rgt"])
-	items = frappe.db.sql("""
-		select i.name as item_code, i.item_name, bin.warehouse as warehouse, i.has_serial_no, i.has_batch_no
-		from tabBin bin, tabItem i
-		where i.name=bin.item_code and IFNULL(i.disabled, 0) = 0 and i.is_stock_item = 1
-		and i.has_variants = 0 and exists(
-			select name from `tabWarehouse` where lft >= %s and rgt <= %s and name=bin.warehouse
-		)
-	""", (lft, rgt), as_dict=1)
+	items = frappe.db.sql(f"""
+		select
+			i.name as item_code, i.item_name, bin.warehouse as warehouse, i.has_serial_no, i.has_batch_no
+		from
+			tabBin bin, tabItem i
+		where
+			i.name = bin.item_code
+			and IFNULL(i.disabled, 0) = 0
+			and i.is_stock_item = 1
+			and i.has_variants = 0
+			and exists(
+				select name from `tabWarehouse` where lft >= {lft} and rgt <= {rgt} and name = bin.warehouse
+			)
+	""", as_dict=1)
 
 	items += frappe.db.sql("""
-		select i.name as item_code, i.item_name, id.default_warehouse as warehouse, i.has_serial_no, i.has_batch_no
-		from tabItem i, `tabItem Default` id
-		where i.name = id.parent
-			and exists(select name from `tabWarehouse` where lft >= %s and rgt <= %s and name=id.default_warehouse)
-			and i.is_stock_item = 1 and i.has_variants = 0 and IFNULL(i.disabled, 0) = 0 and id.company=%s
+		select
+			i.name as item_code, i.item_name, id.default_warehouse as warehouse, i.has_serial_no, i.has_batch_no
+		from
+			tabItem i, `tabItem Default` id
+		where
+			i.name = id.parent
+			and exists(
+				select name from `tabWarehouse` where lft >= %s and rgt <= %s and name=id.default_warehouse
+			)
+			and i.is_stock_item = 1
+			and i.has_variants = 0
+			and IFNULL(i.disabled, 0) = 0
+			and id.company = %s
 		group by i.name
 	""", (lft, rgt, company), as_dict=1)
 
+	# remove duplicates
+	# check if item-warehouse key extracted from each entry exists in set iw_keys
+	# and update iw_keys
+	iw_keys = set()
+	items = [item for item in items if [(item.item_code, item.warehouse) not in iw_keys, iw_keys.add((item.item_code, item.warehouse))][0]]
+
 	return items
 
 def get_item_data(row, qty, valuation_rate, serial_no=None):