diff --git a/erpnext/manufacturing/doctype/bom/bom.py b/erpnext/manufacturing/doctype/bom/bom.py
index d0a27613780..ebe6e04ac03 100644
--- a/erpnext/manufacturing/doctype/bom/bom.py
+++ b/erpnext/manufacturing/doctype/bom/bom.py
@@ -373,13 +373,6 @@ class BOM(WebsiteGenerator):
 					).format(item.idx, get_link_to_form("Item", item.item_code))
 				)
 
-			if not item.qty:
-				frappe.throw(
-					_("Row #{0}: Quantity should be greater than 0 for {1} Item {2}").format(
-						item.idx, item.secondary_item_type, get_link_to_form("Item", item.item_code)
-					)
-				)
-
 			if item.process_loss_per >= 100:
 				frappe.throw(
 					_("Row #{0}: Process Loss Percentage should be less than 100% for {1} Item {2}").format(
diff --git a/erpnext/manufacturing/doctype/bom_secondary_item/bom_secondary_item.json b/erpnext/manufacturing/doctype/bom_secondary_item/bom_secondary_item.json
index 04ecebc0f4b..0e5363582e9 100644
--- a/erpnext/manufacturing/doctype/bom_secondary_item/bom_secondary_item.json
+++ b/erpnext/manufacturing/doctype/bom_secondary_item/bom_secondary_item.json
@@ -138,8 +138,7 @@
    "fieldtype": "Float",
    "in_list_view": 1,
    "label": "Qty",
-   "non_negative": 1,
-   "reqd": 1
+   "non_negative": 1
   },
   {
    "default": "0",
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index e67b95d2857..146deb6ea9a 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -554,6 +554,13 @@ class StockEntry(StockController, SubcontractingInwardController):
 		for d in self.get("items"):
 			if d.s_warehouse or d.set_basic_rate_manually:
 				continue
+
+			# Zero-qty secondary items carry no inventory value; skip rate calculation
+			if d.secondary_item_type and flt(d.transfer_qty) == 0:
+				d.basic_rate = 0.0
+				d.basic_amount = 0.0
+				continue
+
 			self._set_incoming_item_rate(d, outgoing_items_cost, raise_error_if_no_rate, zero_valuation_items)
 
 		if zero_valuation_items:
@@ -575,7 +582,10 @@ class StockEntry(StockController, SubcontractingInwardController):
 			cost_allocation_per = frappe.get_value(
 				"BOM Secondary Item", d.bom_secondary_item, "cost_allocation_per"
 			)
-			d.basic_rate = (outgoing_items_cost * (cost_allocation_per / 100)) / d.transfer_qty
+			# Only recalculate when cost is actually allocated; otherwise preserve the
+			# user-entered rate (or fall through to get_valuation_rate below)
+			if cost_allocation_per and flt(d.transfer_qty):
+				d.basic_rate = (outgoing_items_cost * (cost_allocation_per / 100)) / d.transfer_qty
 
 		if not d.basic_rate and not d.allow_zero_valuation_rate:
 			d.basic_rate = get_valuation_rate(