The met office said dust-thunderstorm with isolated heavy falls may also occur at scattered places in Karachi division, Islamabad, northern Punjab, eastern Balochistan and Kashmir.
Khyber-Pakhtunkhwa, upper Sindh and southern Punjab will also receive rain.
The Karachi Metropolitan Corporation has prepared the disaster management plan to deal with the rain emergency.
Meanwhile, the authorities have issued urban flooding warning following rain forecast.
On Sunday, the met department had forecast rain in Karachi in next fourty eight hours, but the prediction changed a day later.
The met officials said fresh weather system of monsoon had entered in Pakistan from India could result in a wet spell in Lower Sindh, Punjab and federal capital Islamabad.