diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1994-fix-mssql-errors.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1994-fix-mssql-errors.yaml
new file mode 100644
index 00000000000..b366bca0fe4
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1994-fix-mssql-errors.yaml
@@ -0,0 +1,4 @@
+---
+type: add
+issue: 1994
+title: "A few issues in the migrator when applying migrations against some versions of MSSQL were resolved"
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
index cd4b3305fb9..c47cc2cd64b 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -78,7 +79,18 @@ public class AddIndexTask extends BaseTableTask {
 
 		String unique = myUnique ? "unique " : "";
 		String columns = String.join(", ", myColumns);
-		String sql = "create " + unique + "index " + myIndexName + " on " + getTableName() + "(" + columns + ")";
+		String mssqlWhereClause = "";
+		if (myUnique && getDriverType() == DriverTypeEnum.MSSQL_2012) {
+			mssqlWhereClause = " WHERE (";
+			for (int i = 0; i <myColumns.size(); i++) {
+				mssqlWhereClause += myColumns.get(i) + " IS NOT NULL ";
+				if (i < myColumns.size() - 1) {
+					mssqlWhereClause += "AND ";
+				}
+			}
+			mssqlWhereClause += ")";
+		}
+		String sql = "create " + unique + "index " + myIndexName + " on " + getTableName() + "(" + columns + ")" + mssqlWhereClause;
 		String tableName = getTableName();
 
 		try {
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropColumnTask.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropColumnTask.java
index 9b1d7816e31..d3930b47611 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropColumnTask.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropColumnTask.java
@@ -53,7 +53,8 @@ public class DropColumnTask extends BaseTableColumnTask {
 			return;
 		}
 
-		if(getDriverType().equals(DriverTypeEnum.MYSQL_5_7) || getDriverType().equals(DriverTypeEnum.MARIADB_10_1)) {
+		if(getDriverType().equals(DriverTypeEnum.MYSQL_5_7) || getDriverType().equals(DriverTypeEnum.MARIADB_10_1)
+		 || getDriverType().equals(DriverTypeEnum.MSSQL_2012)) {
 			// Some DBs such as MYSQL and Maria DB require that foreign keys depending on the column be dropped before the column itself is dropped.
 			logInfo(ourLog, "Dropping any foreign keys on table {} depending on column {}", getTableName(), getColumnName());
 			Set<String> foreignKeys = JdbcUtils.getForeignKeysForColumn(getConnectionProperties(), getColumnName(), getTableName());
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java
index 9d5b3171f3b..ae15fa6c8a7 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java
@@ -116,9 +116,11 @@ public class DropIndexTask extends BaseTableTask {
 					break;
 				case DERBY_EMBEDDED:
 				case ORACLE_12C:
-				case MSSQL_2012:
 					sql.add("alter table " + theTableName + " drop constraint " + theIndexName);
 					break;
+				case MSSQL_2012:
+					sql.add("drop index " + theIndexName + " on " + theTableName);
+					break;
 				case POSTGRES_9_4:
 					sql.add("alter table " + theTableName + " drop constraint if exists " + theIndexName + " cascade");
 					sql.add("drop index if exists " + theIndexName + " cascade");