diff --git a/erpnext/manufacturing/doctype/bom/bom.py b/erpnext/manufacturing/doctype/bom/bom.py
index 065707e7e6d..6029a073961 100644
--- a/erpnext/manufacturing/doctype/bom/bom.py
+++ b/erpnext/manufacturing/doctype/bom/bom.py
@@ -341,13 +341,6 @@ 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.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 39fa55123f4..ad2f69af5d9 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",
@@ -218,7 +217,7 @@
  "index_web_pages_for_search": 1,
  "istable": 1,
  "links": [],
- "modified": "2026-03-11 12:12:29.208031",
+ "modified": "2026-06-16 16:49:19.000000",
  "modified_by": "Administrator",
  "module": "Manufacturing",
  "name": "BOM Secondary Item",
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index ae536b8dc42..55463364a3c 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -1380,6 +1380,12 @@ class StockEntry(StockController, SubcontractingInwardController):
 			if d.s_warehouse or d.set_basic_rate_manually:
 				continue
 
+			# Zero-qty secondary items carry no inventory value; skip rate calculation
+			if d.type and flt(d.transfer_qty) == 0:
+				d.basic_rate = 0.0
+				d.basic_amount = 0.0
+				continue
+
 			if d.allow_zero_valuation_rate and d.basic_rate and self.purpose != "Receive from Customer":
 				d.basic_rate = 0.0
 				items.append(d.item_code)
@@ -1397,7 +1403,10 @@ 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:
 				if self.is_new():