I have a endpoint which is on vlan x and a SNTP server on vlan Y of same cisco switch. I am trying to synchronize my time from SNTP server. endpoint is able to resolve ARP and get the mac of SNTP server but not able to ping/connect to SNTP server. I don't understand why the endpoint is not able to synchronize time from SNTP server, i could not see NTP packets from endpoint.
Since you have refused to provide the requested information that we need to correctly answer your question, and based on your comment, it sounds like you are leaking both layer-2 LANs to the SNTP server, but that doesn't help you with the layer-3 network.
Your host (endpoint), with an address on VLAN X, is trying to communicate with another host (the server), with an address on VLAN Y. The addresses are on different layer-3 networks. A host will use ARP to resolve a layer-3 address to a layer-2 address if both host addresses are on the same layer-3 network. If the destination host is on a different layer-3 network, the source host will use the layer-2 address of its configured gateway. Traffic between different layer-3 addresses must go through a router (the host's configured gateway).
That applies to both hosts in a bidirectional protocol.
If you want a server to be directly connected to both VLANs, you need the switch to trunk both VLANs to the server, and the server interface must be configured as a trunk, and the server must have an address in each VLAN. How you configure the server for that is off-topic here.