You will have to wrap your fields within a form to use the validation plugin and it's a good practice anyway. Also, you can invoke the plugin's validation programmatically and check if the form is valid by doing:

Copyvar $form = $('#your_form'),
    validator = $form.validate({...});

//validate the form
validator.form();

//check if the form is valid 
if ($form.valid()) {
    //form is valid
}

For more options, have a look at the docs.

You want to declare a custom validation method to validate the time format.

$.validator.addMethod('correctTimeFormat', function (value, element) {
    var result = false, m, regex = /^\s*([01]?\d|2[0-3]):([0-5]\d)\s*$/;

    if (m = value.match(regex)) {
        result = (m[1].length === 2 ? '' : '0') + m[1] + ':' + m[2];
    }

    return result;
}, 'Invalid time format.');

And then, require that custom validation method for all input time fields.

$('input[type="time"]').validate({
    rules: {
        value: { correctTimeFormat: true }
    }
});

I hope this is what you were trying to achieve. This took longer than expected but I tried to achieve it. This whole form is custom form. You could have used the existing plugins to achieve it. Any which ways it took much time to figure it out. Consider the question as most of things are working, ignore if something's not what you want.

$(document).ready(function() {

  /* contact form validation */
  var Validator = function(formObject) {
    this.form = $(formObject);
    var Elements = {
      name: {
        reg: /^[a-zA-Z ]{2,20}$/,
        require: true,
        error: "Not a valid name.",
      },

      email: {
        reg: /^[a-z-0-9_+.-]+\@([a-z0-9-]+\.)+[a-z0-9]{2,7}$/i,
        error: "Not a valid e-mail address.",
      },
      phone: {
        reg: /^\(?([0-9]{3})\)?[-. ]?([0-9]{3})[-. ]?([0-9]{4})$/,
        error: "Not a valid number.",
      },

      message: {
        reg: /^(?!\s*$).+/,
        error: "Message field cannot be empty.",
      },
      gender: {
        error: "gender is required",
      },
      selectOption: {
        error: "this field is required",
        required: true
      }
    };

    var handleError = function(element, message) {
      element.addClass('input-error');
      var $err_msg = element.parent('div');
      $err_msg.find('.error').remove();

      var error = $('<div class="error"></div>').text(message);
      error.appendTo($err_msg);
      console.log(element);


      element.on('keypress change', function() {
        $(error).fadeOut(1000, function() {
          console.log(element);
          element.removeClass('input-error');
        });
      });

    };

    /* Select Option */

    this.validate = function() {
      var errorCount = 0;

      this.form.find("select").each(function(index, field) {
        var type = $(field).data("validation");
        var validation = Elements[type];
        if ($(field).val() == "") {
          errorCount++;
          handleError($(field), validation.error);
        }
      });

      this.form.find("input, textarea").each(function(index, field) {
        var type = $(field).data("validation");
        var validation = Elements[type];
        if (validation !== undefined) {
          var re = new RegExp(validation.reg);
          if (validation) {
            if (!re.test($(field).val())) {
              errorCount++;
              handleError($(field), validation.error);
            }
          }
        }
      })

      /* Radio button */

      var radioList = $('input:radio');
      var radioNameList = new Array();
      var radioUniqueNameList = new Array();
      var notCompleted = 0;
      for (var i = 0; i < radioList.length; i++) {
        radioNameList.push(radioList[i].name);
      }
      radioUniqueNameList = jQuery.unique(radioNameList);
      console.log(radioUniqueNameList);
      for (var i = 0; i < radioUniqueNameList.length; i++) {
        var field = $('#' + radioUniqueNameList[i]);
        var type = field.data("validation");
        var validation = Elements[type];
        if ($('input[name=' + type + ']:checked', '#test').val() == undefined) {
          errorCount++;
          handleError($(field), validation.error);
        }
      }

      return errorCount == 0;
    };
  };

  /* Submit form*/

  $(function() {

    $("form#test").on('submit', function(e) {
      var NoErrors = new Validator(this).validate();
      if (NoErrors == true) {
        $.ajax({
          url: this.action,
          type: this.method,
          data: $(this).serialize(),
          success: function() {
            // AJAX request finished, handle the results and error msg
            $('.success_msg').fadeIn().delay(3000).fadeOut();
            $('input[type!="submit"], textarea').val('').removeClass('error');
          }
        });

      }
      return false;
    })

  })

});

body {
  background: #fff;
  color: #333;
  font: 76% Verdana, sans-serif;
}

form {
  margin: 1em 0 0 2em;
  width: 90%;
}

fieldset {
  margin: 0;
  border: 1px solid #ccc;
  padding-bottom: 1em;
}

legend {
  font-weight: bold;
  text-transform: uppercase;
}

label {
  float: left;
  width: 5em;
  padding-right: 2em;
  font-weight: bold;
}

div {
  margin-bottom: 30px;
}

input {
  font: 1em Verdana, sans-serif;
}

fieldset ul li input {
  float: left;
  width: 120px;
  border: 1px solid #ccc;
}

textarea {
  width: 300px;
  height: 200px;
  border: 1px solid #ccc;
  font: 1em Verdana, sans-serif;
}

form p {
  margin: 0;
  padding: 0.4em 0 0 7em;
}

form p input {
  background: #666;
  color: #fff;
  font-weight: bold;
}

div.error {
  clear: left;
  margin-left: 5.3em;
  color: red;
  padding-right: 1.3em;
  height: 100%;
  padding-bottom: 0.3em;
  line-height: 1.3;
}

.input-error {
  background: #ff9;
  border: 1px solid red;
}

.success_msg {
  width: 350px;
  line-height: 40px;
  border: 1px solid green;
  border-radius: 5px;
  background-color: rgba(213, 255, 187, 0.7);
  display: none;
  position: absolute;
  bottom: 5px;
  left: 50%;
  transform: translateX(-50%);
  z-index: 999;
  text-align: center;
}

<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.0/jquery.min.js"></script>
<form action="#" method="post" id="test">
  <fieldset>

    <legend>Contact information</legend>


    <div>
      <label for="firstname">Firstname:</label>
      <input type="text" name="firstname" id="firstname" data-validation="name" />
    </div>


    <div>
      <label for="lastname">Lastname:</label>
      <input type="text" name="lastname" id="lastname" data-validation="name" />
    </div>

    <div>
      <label for="email">Email:</label>
      <input type="email" name="email" id="email" data-validation="email" />

    </div>
    <div>
      <label for="phone">phone</label>
      <input type="number" name="phone" id="phone" data-validation="phone" />
    </div>

    <div>
      <label>Gender:</label>
      <input type="radio" name="gender" value="male" data-validation="gender" />
      <input type="radio" name="gender" value="female" data-validation="gender">
    </div>

    <select data-validation="selectOption">
      <option value="">Select any option</option>
      <option value="red">Red</option>
      <option value="blue">Blue</option>
      <option value="green">Green</option>
    </select>

    <div>
      <label for="message">Message:</label>
      <textarea id="message" name="message" cols="30" rows="15" data-validation="message"></textarea>
    </div>

    <p><input type="submit" name="send" id="send" value="Send" /></p>

  </fieldset>
  <div class="success_msg">
    <p>Form submitted Successfully</p>
  </div>
</form>

Use each:

var isValid;
$("input").each(function() {
   var element = $(this);
   if (element.val() == "") {
       isValid = false;
   }
});

However you probably will be better off using something like jQuery validate which IMO is cleaner.

this may be thrown by white-spaces! isn't it? check this too:

$('#submitbutton').click(function() {
    var flag = true;
    $('input.inputme[type=text]').each(function () {
        if(jQuery.trim($(this).val()) == ''){
            alert("Please fill all boxes");
            flag = false;
        }
    });
    return flag;
});