diff --git a/components/apimgt/org.wso2.carbon.apimgt.common.gateway/src/main/java/org/wso2/carbon/apimgt/common/gateway/dto/JWTConfigurationDto.java b/components/apimgt/org.wso2.carbon.apimgt.common.gateway/src/main/java/org/wso2/carbon/apimgt/common/gateway/dto/JWTConfigurationDto.java
index ef034354fede..6991c61e30d9 100644
--- a/components/apimgt/org.wso2.carbon.apimgt.common.gateway/src/main/java/org/wso2/carbon/apimgt/common/gateway/dto/JWTConfigurationDto.java
+++ b/components/apimgt/org.wso2.carbon.apimgt.common.gateway/src/main/java/org/wso2/carbon/apimgt/common/gateway/dto/JWTConfigurationDto.java
@@ -34,6 +34,7 @@ public class JWTConfigurationDto {
     private String jwtHeader = "X-JWT-Assertion";
     private String consumerDialectUri = "http://wso2.org/claims";
     private String signatureAlgorithm = "SHA256withRSA";
+    private String jwtDecoding = "base64";
     private boolean enableUserClaims;
     private String gatewayJWTGeneratorImpl;
     private Map<String, TokenIssuerDto> tokenIssuerDtoMap = new HashMap();
@@ -58,6 +59,7 @@ public JWTConfigurationDto(JWTConfigurationDto jwtConfigurationDto) {
         this.jwtHeader = jwtConfigurationDto.jwtHeader;
         this.consumerDialectUri = jwtConfigurationDto.consumerDialectUri;
         this.signatureAlgorithm = jwtConfigurationDto.signatureAlgorithm;
+        this.jwtDecoding = jwtConfigurationDto.jwtDecoding;
         this.enableUserClaims = jwtConfigurationDto.enableUserClaims;
         this.gatewayJWTGeneratorImpl = jwtConfigurationDto.gatewayJWTGeneratorImpl;
         this.tokenIssuerDtoMap = jwtConfigurationDto.tokenIssuerDtoMap;
@@ -140,6 +142,14 @@ public void setJwtExcludedClaims(Set<String> jwtClaims) {
         this.jwtExcludedClaims = jwtClaims;
     }
 
+    public String getJwtDecoding() {
+        return jwtDecoding;
+    }
+
+    public void setJwtDecoding(String jwtDecoding) {
+        this.jwtDecoding = jwtDecoding;
+    }
+
     public boolean isEnableUserClaims() {
 
         return enableUserClaims;
diff --git a/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/apikey/ApiKeyAuthenticator.java b/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/apikey/ApiKeyAuthenticator.java
index f5886d7884aa..83732353ffd4 100644
--- a/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/apikey/ApiKeyAuthenticator.java
+++ b/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/apikey/ApiKeyAuthenticator.java
@@ -515,7 +515,12 @@ private String generateAndRetrieveBackendJWTToken(String tokenSignature, JWTInfo
             if (token != null) {
                 endUserToken = (String) token;
                 String[] splitToken = ((String) token).split("\\.");
-                JSONObject payload = new JSONObject(new String(Base64.getUrlDecoder().decode(splitToken[1])));
+                JSONObject payload;
+                if (APIConstants.JwtTokenConstants.DECODING_ALGORITHM_BASE64URL.equals(jwtConfigurationDto.getJwtDecoding())) {
+                    payload = new JSONObject(new String(Base64.getUrlDecoder().decode(splitToken[1])));
+                } else {
+                    payload = new JSONObject(new String(Base64.getDecoder().decode(splitToken[1])));
+                }
                 long exp = payload.getLong("exp");
                 long timestampSkew = OAuthServerConfiguration.getInstance().getTimeStampSkewInSeconds() * 1000;
                 valid = (exp - System.currentTimeMillis() > timestampSkew);
diff --git a/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/jwt/JWTValidator.java b/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/jwt/JWTValidator.java
index 7e418f7e0771..4116e0bc2c1a 100644
--- a/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/jwt/JWTValidator.java
+++ b/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/jwt/JWTValidator.java
@@ -290,7 +290,12 @@ private String generateAndRetrieveJWTToken(String tokenSignature, JWTInfoDto jwt
             if (token != null) {
                 endUserToken = (String) token;
                 String[] splitToken = ((String) token).split("\\.");
-                JSONObject payload = new JSONObject(new String(Base64.getUrlDecoder().decode(splitToken[1])));
+                JSONObject payload;
+                if (APIConstants.JwtTokenConstants.DECODING_ALGORITHM_BASE64URL.equals(jwtConfigurationDto.getJwtDecoding())) {
+                    payload = new JSONObject(new String(Base64.getUrlDecoder().decode(splitToken[1])));
+                } else {
+                    payload = new JSONObject(new String(Base64.getDecoder().decode(splitToken[1])));
+                }
                 long exp = payload.getLong("exp") * 1000L;
                 long timestampSkew = getTimeStampSkewInSeconds() * 1000;
                 valid = (exp - System.currentTimeMillis() > timestampSkew);
diff --git a/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIConstants.java b/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIConstants.java
index c6f3104e5e15..c4dec6155fcc 100755
--- a/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIConstants.java
+++ b/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIConstants.java
@@ -439,6 +439,7 @@ public final class APIConstants {
     public static final String JWT_DEFAULT_AUDIENCE = "http://org.wso2.apimgt/gateway";
     public static final String JWT_CONFIGS = "JWTConfiguration";
     public static final String JWT_HEADER = "JWTHeader";
+    public static final String JWT_DECODING = "JWTDecoding";
     public static final String ENABLE_USER_CLAIMS = "EnableUserClaims";
     public static final String BINDING_FEDERATED_USER_CLAIMS = "EnableBindingFederatedUserClaims";
     public static final String TOKEN_GENERATOR_IMPL = "JWTGeneratorImpl";
@@ -2101,6 +2102,7 @@ public static class JwtTokenConstants {
         public static final String INTERNAL_KEY_TOKEN_TYPE = "InternalKey";
         public static final String TOKEN_TYPE = "token_type";
         public static final String API_KEY_TOKEN_TYPE = "apiKey";
+        public static final String DECODING_ALGORITHM_BASE64URL = "base64url";
     }
 
     public static final String SIGNATURE_ALGORITHM_RS256 = "RS256";
diff --git a/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIManagerConfiguration.java b/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIManagerConfiguration.java
index b7103b4bfee2..88f2ed977c47 100644
--- a/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIManagerConfiguration.java
+++ b/components/apimgt/org.wso2.carbon.apimgt.impl/src/main/java/org/wso2/carbon/apimgt/impl/APIManagerConfiguration.java
@@ -1608,6 +1608,11 @@ private void setJWTConfiguration(OMElement omElement) {
             if (jwtHeaderElement != null) {
                 jwtConfigurationDto.setJwtHeader(jwtHeaderElement.getText());
             }
+            OMElement jwtDecoding =
+                    omElement.getFirstChildWithName(new QName(APIConstants.JWT_DECODING));
+            if (jwtDecoding != null) {
+                jwtConfigurationDto.setJwtDecoding(jwtDecoding.getText());
+            }
             OMElement jwtUserClaimsElement =
                     omElement.getFirstChildWithName(new QName(APIConstants.ENABLE_USER_CLAIMS));
             if (jwtUserClaimsElement != null) {
diff --git a/features/apimgt/org.wso2.carbon.apimgt.core.feature/src/main/resources/conf_templates/templates/repository/conf/api-manager.xml.j2 b/features/apimgt/org.wso2.carbon.apimgt.core.feature/src/main/resources/conf_templates/templates/repository/conf/api-manager.xml.j2
index 329d983da1f0..6f6b49951d59 100644
--- a/features/apimgt/org.wso2.carbon.apimgt.core.feature/src/main/resources/conf_templates/templates/repository/conf/api-manager.xml.j2
+++ b/features/apimgt/org.wso2.carbon.apimgt.core.feature/src/main/resources/conf_templates/templates/repository/conf/api-manager.xml.j2
@@ -80,6 +80,14 @@
         <!-- This parameter specifies which implementation should be used for generating the Token. For URL safe JWT
              Token generation the implementation is provided in URLSafeJWTGenerator -->
         <!--<JWTGeneratorImpl>org.wso2.carbon.apimgt.keymgt.token.URLSafeJWTGenerator</JWTGeneratorImpl>-->
+
+        <!-- Set the JWT decoding method. Options are "base64url" or "base64". The default value is "base64". -->
+        {% if apim.jwt.decoding %}
+        <JWTDecoding>{{apim.jwt.decoding}}</JWTDecoding>
+        {% elif apim.jwt.encoding %}
+        <JWTDecoding>{{apim.jwt.encoding}}</JWTDecoding>
+        {% endif %}
+
        {% if apim.jwt.enable_tenant_based_signing is defined %}
         <EnableTenantBasedSigning>{{apim.jwt.enable_tenant_based_signing}}</EnableTenantBasedSigning>
         {% endif %}