diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
index a6534da7844..9dbea4a3d7b 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
@@ -609,12 +609,14 @@ public abstract class BaseParser implements IParser {
 	private boolean isStripVersionsFromReferences(
 			CompositeChildElement theCompositeChildElement, IBaseResource theResource) {
 
-		Set<String> autoVersionReferencesAtPathExtensions =
-				MetaUtil.getAutoVersionReferencesAtPath(theResource.getMeta(), myContext.getResourceType(theResource));
+		if (theResource != null) {
+			Set<String> autoVersionReferencesAtPathExtensions = MetaUtil.getAutoVersionReferencesAtPath(
+					theResource.getMeta(), myContext.getResourceType(theResource));
 
-		if (!autoVersionReferencesAtPathExtensions.isEmpty()
-				&& theCompositeChildElement.anyPathMatches(autoVersionReferencesAtPathExtensions)) {
-			return false;
+			if (!autoVersionReferencesAtPathExtensions.isEmpty()
+					&& theCompositeChildElement.anyPathMatches(autoVersionReferencesAtPathExtensions)) {
+				return false;
+			}
 		}
 
 		Boolean stripVersionsFromReferences = myStripVersionsFromReferences;
@@ -622,21 +624,20 @@ public abstract class BaseParser implements IParser {
 			return stripVersionsFromReferences;
 		}
 
-		if (myContext.getParserOptions().isStripVersionsFromReferences() == false) {
+		if (!myContext.getParserOptions().isStripVersionsFromReferences()) {
 			return false;
 		}
 
 		Set<String> dontStripVersionsFromReferencesAtPaths = myDontStripVersionsFromReferencesAtPaths;
-		if (dontStripVersionsFromReferencesAtPaths != null) {
-			if (dontStripVersionsFromReferencesAtPaths.isEmpty() == false
-					&& theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
-				return false;
-			}
+		if (dontStripVersionsFromReferencesAtPaths != null
+				&& !dontStripVersionsFromReferencesAtPaths.isEmpty()
+				&& theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
+			return false;
 		}
 
 		dontStripVersionsFromReferencesAtPaths =
 				myContext.getParserOptions().getDontStripVersionsFromReferencesAtPaths();
-		return dontStripVersionsFromReferencesAtPaths.isEmpty() != false
+		return dontStripVersionsFromReferencesAtPaths.isEmpty()
 				|| !theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths);
 	}
 
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5842-json-parser-npe.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5842-json-parser-npe.yaml
new file mode 100644
index 00000000000..4f6f8570ff9
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5842-json-parser-npe.yaml
@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5842
+title: "Fixed a bug where an NPE was being thrown when trying to serialize a FHIR fragment (e.g., backboneElement
+, compound datatype) to a string representation if the fragment contains a `Reference`."
diff --git a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
index 47b73e6d0cc..8964bd244f2 100644
--- a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
+++ b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
@@ -1168,6 +1168,18 @@ public class JsonParserR4Test extends BaseTest {
 		assertEquals(expected, actual);
 	}
 
+	@Test
+	public void testEncodeToString_CompoundTypeWithReference() {
+		Identifier identifier = new Identifier();
+		identifier.setSystem("http://system.org");
+		identifier.setValue("123");
+		Reference reference = new Reference("Organization/1");
+		identifier.setAssigner(reference);
+		String expected = "{\"system\":\"http://system.org\",\"value\":\"123\",\"assigner\":{\"reference\":\"Organization/1\"}}";
+		String actual = ourCtx.newJsonParser().encodeToString(identifier);
+		assertEquals(expected, actual);
+	}
+
 	@Test
 	public void testEncodeToString_Resource() {
 		Patient p = new Patient();